Ok, I've played a bit with some of the C layouts now and here are my new thoughts:
Kestrel C(unlocked)
I haven't played as this ship yet, but I like the design of it(we got a rebel colored kestrel and now a pirate one
).
Layout looks nice, exept for the empty space in the middle of the ship.(It's almost like Kestrel A).
Lanius is nice because you can remove the air from the rooms where the boarders are in and send the lanius to fight them
for extra damage.
Ion Stunner is ok, it's a Ion Blast 1 with 2 seconds longer charge and extra stun, which is nice for boarding because
even if the shields are up, everyone in the shield room will get stunned.
Dual Lasers are ok, they are a good weapon, but I would've liked Burst Laser MK2 more(I can see why it isn't here) so
you have at least one good weapon for the end game ready. Dual Lasers can be a nice support but you want to get more
lasers.
Engi C(didn't unlock it, I was 2 jumps away from reaching the eight sector with the vortex)
Interesting Room Layout with systems, but it could be very weak to beams because of that.
Not many places to remove the O2, but that's probably ok because engis remove fire faster.
Lanius is nice against boarders and can help. 2 Engi's are great.
Dual Lasers are nice, at least this ship has some good starting weapons other than the drone(type A had only a drone and
a great Ion Blast MK2, type B had that slow Heavy Ion and Heavy Laser). Ion weapons are a bit missing here, but it's
still nice.
Hacking works well too because you can remove the shields of a enemy for your drone to hit.
I'm not a big fan of Beam Drones, but it probably deals more DPS than the Laser counterparts.
Defense Scrambler is the biggest win here. Anti Combat Drones destroyed the Drone use on Drone based ships. This is the
reason why I'll use this instead of the A ship in advanced edition.
Federation C(Unlocked)
I did one run with this and from what I've seen it doesn't work at all. Flak takes ages to charge, Mantis and Human
aren't that great for boarding, Zoltans might be nice for the damage, but it doesn't work.
Ok, the ship Layout isn't that much different than the other Federation Ships, it's a bit like the Type A but with more
random holes. You can remove the air very well here, there are doors almost everywhere exept for the middle.
Flak Gun is ok, not sure if it ignores shields like the beam does.
Other than that the ship doesn't have any other weapons, but a teleporter, so this was made for boarding.
You start with a Mantis(which is probably what I should use for boarding), 2 Zoltans(which now blow up on death, like
their green cube friends) and 1 Human.
I'm guessing that this ship was made to tell you about the new Zoltan Gimmick, you get a level 2 Clone Bay for that, but
this doesn't make leveling any better.
Emergency Respirators are ok, but why is this here and not on a Lanius Ship ? Backup DNA or something that doesn't make
your crew loose Skill on cloning would probably be better. It's there for AI ships.
I'm going to try what Ragwortshire said, that looks like it could work. Maybe we need to learn on how to play the ships.
Mantis C(not unlocked yet, getting bad luck with Mantis B

)
Looks like a interesting ship, the color is a bit strange but very nice.
This ship has doors everywhere, nice against boarders and fire.
I get the idea of the ship, it's a mix of A and B, taking the great weapons and crew but keeping the big teleporter and
boarding from B.
The wiki doesn't have the data about the stun bomb up and I only used it once. As far as I remember, it does 1 Ion
Damage, but stuns the crew for a longer amount of time. I don't know if it stuns your own crew.
Lock Bomb is great for keeping the enemy in the room with the lanius, but what is this crystal weapon searching here ?
Getting the archievement for that would be nice but this isn't the crystal cruiser. An other question would be on why
this has a level 2 clone bay ? Did they think that the mantis and lanius can't work together(because of the air), so
they will probably both take some extra damage, so the cloning is needed to keep the enemy ship attacked ?
I don't know but it's nice.
Crew is ok.
The Mantis is there for boarding, so is the Lanius. The engi is there, like the ship A for fixing stuff and keeping the
ship manned. The problem here is that the ship wants to show you 2 boarding types, Lanius and Mantis. You only start out
with one of the crew and getting Lanius can be difficult. They also don't mix that well because your mantis needs air.
Zoltan C(Unlocked)
Gimmicky Ship.
This Ship starts out with only 2 power and needs extra scrap for the next 3 power upgrades(30 instead of 20), a easy way
to bypass this is to accept the trade on the random events that upgrade the reactor power by 1.
You get 4 Zoltan Crew, which is 1 more than the default, an other nice bonus. To use this ship you need to use the
Backup Battery, which is already at level 2 and doesn't use any power !. Wait for your Charge Ion to Charge up, shoot,
get the battery active and start the drone.
There isn't a good way to remove the O2 from the shields(engines or the clone bay. A big room(which is probably used for
cloak) is in the middle of the ship, which can split up the ship if you get hacked there(subsystems are down there,
systems are up).
All Zoltan Ships Start out with a beam weapon, this one starts with a beam drone instead. It's a lot like the Engi A,
exept getting an other weapon working here won't be easy.
Charge Ion isn't that bad, but not that good either, it only does 1 ion damage and charging it up takes some time.
The Beam Drone is nice, I got a second one on my run and that was very good. The only problem are the anti combat
drones, which destroy this ship, so maybe it would've been way better if this had the beam 2.
This ship might not look very strong but I had a good run with it, might be one of the better(good chance to win) ships.
Slug C(not unlocked yet)
Slugs were always mean, and mind control+hacking are very fitting for this ship.(I'm guessing that one ship would've
gotten the mind control and one the hacking if we got multiple ships, but they had to put both into one). This makes
this ship interesting because you can only get one system from the old ones(teleport, cloak OR drones), Teleport works
well with hacking and mind control, but cloak is needed to evade missiles and for the flagship... then again, drones
could be very nice...
It's a bit difficult on what you want to get because you can't remove systems.
This ship's door layout are good, exept for the missing doors on the right bottom corner, it isn't symmetrical because
of that.
3 Slugs are nice, not that much but more than layout A.
Stronger Doors are a part of every slug ship, which makes them good against boarders.
Chain Laser is ok, I don't like the high charge time on the first few shots, nothing that will be useful for too long,
but useful as a support weapon later on.
Rock C(not unlocked yet, failed at sector 7 with type B)
This ship looks interesting, modern but with that crystal design.
2 Rocks are good and 1 Crystal is epic, now you can finally get the Crystal Cruiser with less trouble(exept that you
still need to unlock layout B, which needs 2 archievements, and one of the 3 is finding the crystal sector).
Not many doors to remov the air, only some on the front and on the back. Lots of holes, looks almost like this ship is
made out of 2 parts connected.
Swarm is a very good weapon. Charge time is ok, 1 damage for a missile might be a bit bad, but getting 3 for one shot is
nice and doesn't let you run out of missiles that fast. The area of effect isn't that good of a idea because it makes
this weapon miss sometimes or hit other rooms that you didn't want to.
Crystal Heavy Laser is like the heavy pierce laser from Rock B, so it's ok but you need to get a alternate weapon if you
want to complete the game with it.
Looks like a good ship with surprisingly small room layout.
Stealth C(unlocked)
Stealth C is.. strange to play as.
Instead of a cloak or shields you start with nothing. the Shield overcharger and the anti combat drone are going to help
you to play with this ship.
Room layout is a bit strange and has holes in the middle of it like all AE ships. If it didn't have the hole in the
middle, then it wouldn't have that many doors but with that it has enough.
1 Human, 1 Rock and 1 Slug are nice, but nothing too special.
Charge Laser is a edited version with shorter cooldown and only 1 power use. This makes it a nice replacement for the
dual lasers because you can shoot it when you want. The only disadvantage is the 1.5 seconds longer charge time.
Mini Beam isn't that great but ok, nothing special about it.
Drones are a bit special here. You have 3 Drone Slots instead of 2 and one of them is a modified drone.
Shield Overcharger is a nice Drone, but it wasn't made for starting, it's more a endgame drone for extra shields, adding
a extra layer every 8 seconds and only for that beacon, but here it doesn't work too well.
At first I thought that you had to activate it in battle, which somewhat works. Then I tested activating it before
battle and then jumping there(so you have enough power for the anti combat), but that doesn't work.
After some runs I finally understand how to use it:
You need to know the enemy weapon charge times and time the drones.(like you time the cloak) The shield works like a
zoltan shield, so you need to avoid ion because it doubles the ion damage on the shield. This Drone is modified to only
use 2 instead of 3 power, nice for this ship and useful for endgame if you get there.
Anti Combat Drone is very good because that was one of the problems on the other stealh ships. The problem is that you
only start out with 2 drone power, so you can have anti combat or shield but not both.
Long Ranged Scanners are like the ones on every stealth ship, nothing special.
Most of the C ships look like very good new ships, others are a bit strange to play, maybe we need to learn on how to play them ?(Does this mean that the vortex has a use ?)