Ok here are my two cents:
Drone Uplink Jammer: I haven’t tested it, but if the 20% chance of failure fires, I would suggest that the 2 power used for it not be lost. Perhaps I cannot depend on the bonus of the Augmentation, but I should always be able to depend on my Power’s being useful.
Thats already how it works. Can you take a screenshot next time it uses power even though it failed? That might need fixing.
Advanced Plating: I suppose there is fundamentally nothing wrong with this, but one of the primary problems with Hacking/Mind Control isn’t even so much their main effects, but their passive effects of knocking out a main system/distraction (Mind Control) or slowing a system considerably though loss of crew bonus (Hacking). In my opinion, it would be better to have this as a 2 or 3-power system (probably 2 power) that kills Hacking/Mind Control utterly. A secondary option would be to have multiple Blue options available - pay 1 power to knock the system to 1 power; or pay 3 power to eliminate Mind Control/Hacking entirely. Furthermore, since I’m quite unhappy with the Teleporter Disruptor (read on…), integrating that here as well as a separate option could make this a uniquely versatile Augmentation, as long as we curb it to hitting one or the other, not both.
In generall I can't add more multi-options augs since that has the potential to break the text box ui.
Subspace Scanner: This actually is frighteningly useful for only 30 Scrap and 1 power - being able to knock out cloaking is amazing! If possible, I’d suggest 2 power to kill cloaking and 1 power to use sensors in a nebula, or even 0 power for sensors in a nebula, and maybe a price increase to 40. Throw the bonus of the Lifeform Scanner on and we have a strong, good deal as long as its pricey enough.
Under consideration. Not the fuse though.
Targetting Jammer: As with the Drone system, while this is powerful indeed, if it should fail, I want my 2 Power back.
Same as above.
Teleporter Disruptor: Again, as with the Radiation Projector, the issue here is that CE actually does have a fair number of enemy ships with level 3 Teleporting. Add on to this that boarders are usually not that hard to deal with even with a fairly pathetic defending crew, and I just don’t understand why I would even want this Augmentation.
Suggestion: Remove this Augmentation from the game! OR, just make it not purchaseable in Shops but still droppable normally (Is that even possible?), so it doesn’t take the space of something that is actually useful. This would make it a unique Augmentation, and then for a single power it would be reasonable to have it utterly lock down enemy Teleporters, even if they were level 3. However, better it is removed than available in the shop. An additional thought is that it can offer a Blue option to knock out boarders that come as part of events in random places when jumping through the sector.
A fan favourite, this will likely remain as it is. Tons of blue options and fairly useful for its price.
Internal Effector: I haven’t actually seen this Augmentation myself so I can’t comment, but it seems cool enough.
Slug B starts with it.
AI Avatar Generator: The problem with actually bothering to purchase this (unless you’re really Really REALLY desperate for crew…that is, you have 1 crewman by Sector 7) is that the price demands for creating the crew, in addition to purchasing the Augmentation, is such that by the time you’ve creating 2 AI Avatars, you could have just purchased 2 other much more useful crew directly from the shops, instantly, and then used those empty beacons for something more useful when you hit them, besides having space for some other Augmentation. And God forbid that you should be lacking the 15 Scrap to make the Avatar when you get there. Not a reasonable investment, in my opinion.
Suggestion: AI Avatars are always generated for free, but the price of the Augmentation can remain the same, or at most be reduced to 50 Scrap. Alternatively, this could also be an item that is never purchaseable from the shop to make it a unique item for generating Avatars for free, with a decent sale price of 30 Scrap - if you can buy other crewmen anyways from the shop instead of this Augmentation, no need for it to be taking up the space of something more useful. My preference though would that this be not available in the shop and remain instead as a special Augmentation.
Price change under consideration. Failure will be less severe. Other than that its free crew forever, worth the prices in my opinion.
Ammo Manufacturer: I’d suggest that this never show up in shops. When you can build it anytime you want at an Empty Beacon, it just doesn’t need to be taking up a slot in the shop where something more useful could be residing.
Drone Manufacturer: I’d suggest that this never show up in shops. When you can build it anytime you want at an Empty Beacon, it just doesn’t need to be taking up a slot in the shop where something more useful could be residing.
Under consideration, although I generally disagree that everything you see in the shops need to be instant buys basically. That doesn't event apply to vanilla by a long shot.
FTL Fuel Recycler: This Augmentation could easily use a cost increase to 50 or even 60. Unquestionably pays off for itself, and I’ve definitely never felt at a loss for Fuel ever again when I have one around. Awesome Augmentation!
Good as is, as other have pointed out.
Hull Repair Kit: This could be interesting if it was combined with the Repair Arm. As it stands, even with the CE buff to the Repair Arm, the Repair Arm still doesn’t seem worth it (neither in later sectors where you lose tons of money; nor in earlier sectors where repairing is too cheap to matter, but I guess all that means is that proportionally the healing-to-money is the same…perhaps we could just drop it to 8% and leave it at that); as for the Hull Repair Kit, getting the best of out of it requires either too much time, or too much Scrap, or at least it certainly isn’t as useful as a Hull Repair Drone. What I might suggest is a combination of the two, where the Hull Repair Kit always repairs one (exactly one) Hull at no cost to the player for every acquisition of Scrap, and then additionally you get the normal Hull Repair Kit bonus if you should want to use it (no changes to that) - this way you’re getting some free but non-major repairs that are quite useful, and if necessary you can make bigger repairs on the way for the appropriate cost.
Emergency repairs don't cost time and repairs are as economic as shops, more so in the late game. Good as is. Repair amount of Repair arm can't be changed.
On-Board Assembly Line: I would suggest that this take no time to use. You’ve already effectively lost a jump by hitting an empty beacon, and we’re going to double the fleet’s next jump, too? All this for a product that we can’t even guarantee we’ll be selling at a decent price at any point, much less right away, and even then it may cost you another jump at the Store to sell it. This is rarely, if ever, worth it, and I certainly can’t imagine wanting to bother purchasing this from the shop.
Suggestion: Make this never available at the shop, but a potential thing that can be acquired. Costs no time to make trade goods, and that which is produced is on the more decent end of things more likely than not. Reduce “cost” to 20 (you don’t sell it for much, but you could sell the products well enough)
In generall, you don't loose a jump effectively through empty beacons. Empty beacons are always there, statistically you'll always encounter them and everything that CE adds to them is a free bonus. Empty beacons are simply a part of the game you'll have to work with and CE used them to give you free stuff basically. Time cost reduction is under consideration though, simply cause I like to boost trade. Also making things available only as loot but not as as store content is somewhat finicky and not really an option.
Advanced Navigation AI: Definitely awesome the new way it is set up. However, since we have so many different Augmentations in CE and it can be hard to find any one in particular (there’s no way to “depend” on RNG short-term or long-term in CE like you could in Vanilla, because there’s so many options), I’d suggest combining this with the FTL Recharge Booster to make a single Augmentation, as it would both be an appropriate final edition, and it would cut down on clutter in the shops. FTL Recharge Booster is only useful anyways if you’re losing, which isn’t something you want to be counting on: remember that the best defence is a good offence. *** This may not work. Possibly put FTL boost with FTL Fuel Recycler or Beacon Access Kit.
Not possible.
Beacon Access Kit: Solid Augmentation. Suggest deleting Distraction Buoys entirely, as they are overshadowed by the Beacon Access Kit, and one less unnecessary Augmentation would reduce clutter in the shops. *** (maybe put FTL Speed boost here)
For the deletion of vanilla content, refer to Twinge or Subset Games please.
Bounty Hunter Database: The rewards for completing these quests are actually pretty terrible, but the idea is cool. It would be neat if the rewards for Low/Medium/High included in addition to Scrap, an appropriate level of Weapon/Drone/Augmentation to go along with it. Because in the end, what are you really gaining? That one jump that could have been another beacon will probably yield a different battle, anyways, which means you’re no less behind, but you ARE more behind from not using your Sector Entry beacon for some other kind of purpose, so in the end, the Bounty Hunter Database just ends up costing you 30 Scrap and potentially a mission from one of your crewmen. So again, buff the rewards, or it isn’t worth it.
Free gear every sector wont be happening. You gain a guaranteed double reward beacon as opposed to a uncertain beacon that might or might not have a fight (most of the time a single reward fight). Its a net gain, although not as good a econ aug as others.
Cargo Teleporter: Way too expensive to facilitate a feature of CE that’s often not profitable anyways or at the best unwieldy. This deserves a price of 40 at most, but more reasonably 30, only to bring Trade to a level that could be considered on par.
Under consideration although it pays for itself fairly quickly already. Largely depends on how well you know the trade system.
Combat Simulator: This Augmentation is, quite frankly, just a hindrance to useful things popping up in stores, and tends to be useless, anyways, as most kinds of crew experience are already attainable by normal means or by finding a single ship that can’t penetrate your shields. The only decent thing that can come out of it is Repair experience. When it comes right down to it, I honestly have to suggest that this Augmentation is so awful, that it shouldn’t exist in the game whatsoever, neither in the shop, nor as a random drop. Please delete it.
Under consideration.
On-Board Science Lab: This Augmentation really isn’t distinctive enough from the On-Board Assembly Line to justify being its own Augmentation, and additionally, the products that the Science Lab yields aren’t even that good. I think we could go a few ways with this so it isn’t a burden on the store.
Suggestion 1: Delete the Science Lab entirely. It isn’t worth the clutter on the store or on a decent drop.
Suggestion 2: Merge the Science Lab with a semi-unrelated Augmentation, like the previous Mapping Computer. A Science Lab is most appropriate for mapping the sector, and also for extracting resources here and there. They would blend well together to make a single Augmentation that’s less burdensome on the store while having multiple useful but not terribly overpowering tasks. I’d still keep the cost at 30 Scrap, though, because I still don’t think it would be worth more than that.
Might merge with mapping computer.
Requisition License: This Augmentation is just plain awesome for its cost (much like the FTL Fuel Recycler). There are otherwise so many Civilian ships in CE that between these and empty beacons, sometimes an entire sector can be visited while seeing barely a piece of Scrap, which is horribly disabling (and I think, in the end, a design flaw, but I’ll ignore that as I’m not really focusing on events here). This undoes the problem so well that it’s easily worth 40 or 50 scrap to purchase it - 20 is definitely too low.
Under consideration.
Adaptive Gel Suits: I’m not super fond of the nerf here because this was already a niche item in the first place, so I think buffing it back up again would be appropriate. However, I’m just reading the description right now, and the description seems weaker than the actual effect. Perhaps we want to review this one…
Gives many blue options now and can be engineered.
Advanced Targetting Computer: Increase cost to 50 - this is way too good for merely 40 Scrap.
Install Twinges balance mod then.
FTL Recharge Booster: As previously mentioned, delete this Augmentation, and blend it into the Advanced FTL Navigation with its 30% FTL bonus.
Not possible
Improved Internal AI: Keeping your Drones active even when Drone communication is scrambled is what makes this worthwhile. Does anyone actually use it to increase internal Drone speed…? That part of this Augmentation is so bad that if it were about that alone, it would never be worth using. For that reason, being able to fabricate internal Drones isn’t terribly exciting, save the possibility of Boarding Drones. It could be fun if this increased the speed of external Drones, or the firing rate of Defensive Drones. Drone Scrambling does come up from enemy ships, but it’s not so common that I’ve felt that I ever needed to invest in this Augmentation, even though anti-scrambling is good. Nevertheless, this Augmentation feels like it needs something. It’s okay, but it needs something. (see below - in my commentary on Fire Suppression, which is ridiculously expensive for its effect, anyways, this would make a wonderful blend here) *** This may not work. Internal Generator could blend with this very interestingly instead. Fire Suppression could only realistically otherwise go with Science Lab or Advanced Plating.
Fusing two augment effects is not possible through modding.
Scrap Recovery Arm: 8% is decent with a price reduction to 40 Scrap. I agree.
Yo for the record: These price and stat changes where only done because that stuff can be engineered now.
Shield Charge Booster: This Augmentation is still pretty awful, so awful that it almost needs deletion. Barring very unique circumstances, most of which occur at times when you will never have access to this Augmentation (ex. sector 1 ship with a Laser Cannon and a Mini Beam to recharge the Shields before the Mini Beam hits), the only really meaningful time/times this ever could come into play is when fighting a ship with a heck of alot of Drones, particularly the Flagship #2. Am I really going to invest in an Augmentation for a single endgame battle, and maybe one other? I don’t think so. Let’s discuss some other possibilities.
Suggestion 1: Delete this item - it’s pointless and just takes up space in the shop.
Suggestion 2: Make the boost much stronger, like 30 to 50% range, so the shield regeneration is sufficiently strong to really impede attacks other than focused volleys. Of course, it’s still not helping against Missiles and Bombs.
Suggestion 3: Since it mainly fits into the same category, the 15% Shield Boost could be integrated into the Reverse Ion Field, which is about protecting your Shields, anyways. Since you lose your Manning bonus at one point of ionization, the 15% Shield Boost would be useful in keeping the remaining Shields up while recovering from Ionization. The consequent combined Augmentation would need an appropriate increase in cost, however. But I think that this is the best solution, and it eliminates one more Augmentation to free up space in the shops.
Refer to Subset or Twinge.

I now plenty of hard streak runs that consider this an instant buy, so it can't be that bad.
Titanium System Casing: While the buff to this Augmentation in CE was most appropriate, in all honesty I think even further improving it to 30% is the right way to go. CE depends on more weapons than Vanilla that don’t even harm systems, which detracts from this Augmentation’s effectiveness-in-point: when it actually is being effective and you really think about it, 30% isn’t that much, and a single point where you don’t want it really hurts, so having 90% at max is strong and feels reasonable.
Under consideration.
Burst Mark IV: Same fire chance as Mark II; fires 7 shots instead of 5; price increase to 105 Scrap.
Sounds great, until it is fired at you...
As for weapons in generally, some stuff is under consideration. Overall I won't be messing with rarity too much and I won't make wide changes to vanilla gear. From my experience, that just ends up causing irritation for now players. I also don't fully understand how rarity works, my best guess is that shops select rarity levels for slots first and then populate that slot with gear from that rarity level. This would explain how the negative prefixes in early EL where so prevelant, but I'm not sure if it really works that way. But it definitely feels like the stuff of same rarity actually competes with another in store, so making something you'd like to see less more rare actually has the other rare stuff become less likely as well. In general I simply keep rarity in line with the theoretic parent asset of each gear piece.