Hokay, so here's that side-by-side comparison between the vanilla list of augments and the CE list that I promised:
Note that I have excluded augments that can't be bought in store, since store-bought augments are the topic being discussed here. I've also included Titanium System Casing and Improve Internal AI in the CE list despite not being 100% sure those are in fact sold in CE stores. Please let me know if I got that wrong.
Note also that my ranking of each augment is obviously somewhat subjective, but given that that same subjective opinion is being applied to both lists, the data we get out of it should still be somewhat valid for the purposes of directly comparing the two lists, and I also encourage others to modify the lists or generate their own if they strongly disagree with me regarding a large number of augments.
With that said, here's how I decided to rate any given augment:
Good augments: Good augments are augments that are virtually always helpful in one way or another, typically through a direct combat (such as Pre-Igniter) or economy (such as Scrap Recovery Arm) boost. Note that I decided that economy-boosting augments that are not useful to purchase in the late game, despite being more situational than the combat augments, can still be considered "good" and are not
so situational as to require bumping them down to the next tier.
Good (situational): Good but situational augments are most commonly the augments that provide a big boost to a particular system you may or may not have, such as Drone Recovery Arm. These are very helpful if you find them under the right circumstances, but useless if you find them under the wrong circumstances.
Moderato augments: Most moderato augments are those that can always potentially benefit you, but much less so than the good augments, typically due to having some significant drawback (such as On-Board Science Lab requiring you to frequently accept doubled fleet pursuit to get the most use out of it), or simply not providing as large a benefit as a "good" augment (such as Titanium System Casing).
Moderato (situational): Moderato and situational augments are to moderato augments as good but situational augments are to good augments. These are of lesser or questionable benefit
and require specific conditions to be met in order to be useful.
Highly situational augments: As it sounds, these are the augments that are typically only useful around the margins, in fringe or edge cases the player should not encounter very often unless something is already very wrong, or are simply flat-out uncommon.
Bad augments: These are augments that are either of such questionable utility that I'd never consider them worth the expense of purchasing, or which actively harm the player's chances of winning a run. There are actually remarkably few of these in FTL.
And now for the lists themselves:
Vanilla augments:Good augments:Automated Re-loader
Long-Range Sensors
Scrap Recovery Arm
Weapon Pre-Igniter
Good augments (situational):Drone Recovery Arm
Explosive Replicator
Reconstructive Teleport
Stealth Weapons
Zoltan Shield Bypass
Moderato augments:Distraction Buoys
Reverse Ion Field
Shield Charge Booster
Moderato augments (situational):Backup DNA Bank
Battery Charger
Lifeform Scanner
Highly situational augments:Adv. FTL Navigation
Defence Scrambler
Emergency Respirators
FTL Jammer
FTL Recharge Booster
Bad Augments:Fire Suppression
Hacking Stun
Repair Arm
Total:Good: 4/23 (17%)
Good (situational): 5/23 (22%)
Moderato: 3/23 (13%)
Moderato (situational): 3/23 (13%)
Highly situational: 5/23 (22%)
Bad: 3/23 (13%)
CE augments:Good Augments:Advanced FTL Navigation
Advanced Targeting Computer
Bounty Hunter Database
Hull Repair Kit
Ion Field
Long-Range Sensors
Mapping Computer
Requisition License
Scrap Recovery Arm
Sector Scanner
Targeting Jammer
Weapon Pre-Igniter
Good augments (situational):Advanced Cloaking Field
Cargo Teleporter
Drone Recovery Arm
Explosive Replicator
FTL Fuel Recycler
Internal Generator
Reconstructive Teleport
Subspace Scanner
Teleporter Disruptor
Zoltan Shield Bypass
Moderato augments:Anti-Ship Battery
Beacon Access Kit
Distraction Buoys
On-Board Assembly Line
On-Board Science Lab
Radiation Projector
Reverse Ion Field
Shield Charge Booster
Titanium System Casing
Moderato augments (situational):Ammo Manufacturer (engineerable)
Backup DNA Bank
Battery Charger
Drone Manufacturer (engineerable)
Lifeform Scanner
Highly Situational Augments:Adaptive Gel Suits
Advanced Plating
AI Avatar Generator
Combat Simulator
Defence Scrambler
Drone Uplink Jammer
FTL Jammer
FTL Recharge Booster
Improved Internal AI
Bad Augments:Fire Suppression
Hacking Stun
Repair Arm
Total:Good: 12/48 (25%)
Good (situational): 10/48 (21%)
Moderato: 9/48 (19%)
Moderato (situational): 5/48 (10%)
Highly situational: 9/48 (19%)
Bad: 3/48 (6%)
At face value, it may seem like the CE list is completely fine, as it has a higher proportion of good augments as a raw percentage than the vanilla game. However, while making up the two lists I noticed that CE has a lot more augments that may, at any given point in a given run, fall into the category of "not what I need right now". These include redundant augments that all do a similar thing (Long-Range Senors, Sector Scanner, and Mapping Computer being the most egregious example), augments that are only at the their best in the early game (such as Cargo Teleporter and Bounty Hunter Database), and augments with drawbacks that may make the player think twice before picking them up (such as the ASB, which I have never purchased again ever since losing a hard-fought Zoltan C run to the Flagship's third form when they were suddenly able to hack the ASB and make it shoot at me as well. Other examples include AI Avatar Generator with its failure chance, On-Board Science Lab with its fleet pursuit cost, and so-on).
All of these things can serve to "squeeze out" augments the typical player will truly want, making them less likely to appear even though good augments as a general rule may be more likely to appear because they exist in greater proportion in CE (though modified by the rarity values, which are not reflected in my list as I didn't know where to find all of the values for both vanilla and CE). This creates a feeling in the player that augments in CE are worse than they actually are, and even I am not immune from feeling this way as my earlier posts where I said I felt drones and augments had it worse than weapons demonstrates. Having created these lists, I do still think a little bit of controlled merging and pruning would do the augment list good, but one need-not go at with 100% of Gidoza's fervour, even though I do admire his enthusiasm.
Although I acknowledge the reasoning behind not wanting to change the vanilla augments any more than you already have, one possible change that none-the-less immediately comes to mind is giving Lifeform Scanner the benefits of Subspace Scanner and removing Subspace Scanner, in much the same way that Adapative Gel Suits work as compared with vanilla's Emergency Respirators (or Improved Internal AI compared to Drone Reactor Booster, or any of the race-specific augments that in CE enable piracy, slavery, and/or betrayal of ceasefires, etc.), wherein it does the same thing as vanilla, but plus other stuff as well.
So yeah, that's the side-by-side. Once something resembling final decisions have been reached regarding augments, I'll probably create the same kind of list for drones and then another for weapons. I've said before and I'll say it again that I've always thought the game balance is remarkably good in Captain's Edition, and even better than vanilla in many ways (especially when it comes to the starting ship loadouts), but there's always something that can potentially be tweaked, and I'm hopeful we can find suitable ones, in much the same way the Stealth B and Zoltan B were able to be suitably re-balanced the last time I was making a lot of posts here. Failing any of that, though, I hope my lists were at least momentarily interesting to read...
If you made it this far without getting bored, I thank you for your patience.