AWKWARD ZOMBIE

I haven't tried the Mantis ships yet but the few C layouts that I got so far (Kestrel C, Osprey C, Zoltan ship C) are kinda universally worse than their respective Bs.
The Zoltan C ship especially. It has a whooping 3 energy bars (+ 4 from your crew which is technically 3 cause you need a pilot) for god's sake and buying a new one costs 30 from the start. You're supposed to entirely rely on your zoltan crew powering up your stuff. Which would be fine if they didn't only give you a beam drone and an ion weapon that both cost you 2 energy each. So you use 4 energy already just to be able to attack enemies, have to waste 1 potential energy on a pilot so you at least have the possibility to evade, so you can either have 1 bar of shields and zoltan shield with 0 chance of evading or 2 bars of engines and only the zoltan shield. And you're fucked if you come across an enemy ship that has anti drone drones.
Guess what my first encounter was.
So yeah, what the hell.

The C ships I think are supposed to universally be "experimental" ships, that take their gimmicks to the maximum, and don't come with any guarantees.

Also why is the crystal cruiser quest so ridiculous? Every time I start it, it's bodaciously impossible to finish. I start it on like the 6th sector, find the stasis pod, then in the same sector I find the zoltan research facility to get my the crystal guy. But then you need to go to the rock homeworlds for the next part, and oh hey I already passed that like 3 sectors ago...

Yeah that quest takes the luck aspect of the game up to ridiculous.

So, has anyone managed to beat the game with advanced content on? I can only manage to get to the flagship's third form, and then it mind controls my pilot or something and turns my evade to practically nothing.

I like the new Lanius cruiser though. I just open all doors except the one my human is in and that makes fighting intruders really easy.

Still haven't gotten the crystal cruiser though. Came close once, but I decided to help with giant alien spiders and lost my crystal crew member.

I've beat the game a few times I think, one of them was the one time I actually got a mantis ship to work (Mantis B I think.).

I nearly beat it with the stealth cruiser, but it got me with like 3 health left.

I've never managed to actually beat the game. I've gotten to the flagship enough times but never with a decent loadout.

I won once with a perfect cinematic victory. One health point left, rooms on fire, quite clearly on my last leg, I don't remember the state the flagship was in but I needed all my lasers to hit against all odds... and they do.
I guess I can just assume that since their mission was completed my crew must have IMMEDIATELY evacuated or something.

I would have one for the first time today if it weren't for poor luck with the boss map layout. Had to try and fight through three Rebel Controlled Beacons to get to the flagship with no other way to go. Those elite fighters will wreck you thoroughly. I did get to have some fun with the Bio-beam weapon thing. Was also the first time I just had scrap to spare more or less, was able to upgrade my ship twice as much as I would normally with two drones and full weapons. Now to bide my time with Bit.Trip presents... Runner 2: Future Legend of Rhythm Alien.

Yeah the boss would be a lot more possible if you could actually use the repair stations. Every single time without fail, by the time you finish the first part of the boss and need a repair, all 3 of the repair stations are gone, overrun by a single rebel scout or whatever.

I just had a very close victory against the flagship, for my first victory using the federation cruiser. (Layout A)

After a kind of meh first few sectors, I got a Glaive Beam from an event, which synergized perfectly with my stuff. Pierce shields with burst laser mark 2, wreck em with glaive beam, artillery beam providing fantastic support. The entire time, I was looking for a solid third weapon, like maybe another burst laser mark 2. Unfortunately, I could never find a worthy weapon to fill that slot, so I ended up filling it with just a normal 2 shot burst laser, but it did it's job well enough. I also picked up a defense drone mark 1 at one point.

My run was plagued the entire time with losing crew members in various ways, but I managed to recruit enough new members to fill in the gaps, plus a little.

My goal for the run was to locate the rock homeworlds and possibly do the quest to unlock the rock cruiser, and I did enter the rock homeworlds, but couldn't find the beacon for the start of the quest , which was disappointing. I decided to try my luck at the boss though, since it was a pretty solid run. I figured i'd get dominated by the flagship though.

The first two phases of the fight were a total curbstomp. It hacked my drone system, so my defense drone was useless, but after a few volleys, in each phase, the flagship just melted under my firepower.

The third phase though, is where there was a problem. It's boarding dominance focus proved to be just about too much for me. Between mind controlling my weapons man to kill my zoltan and chunk the weapons system, and the waves of boarders they sent, and the power surges just at the right time to turn the tides, I thought I wouldn't be able to get my weapons running well enough to touch the enemy.

I was wrong. Somehow, I think they stopped mind controlling, possibly due to a lucky artillery beam. Also, all their boarders were sent for the piloting and engines, the far side of the ship from the weapons system. So I repaired the weapons, and with a few volleys, I beat the flagship, surviving with just 4 hp.

TL;DR: average FTL run in all aspects

I demolished the flagship pretty hard on easy mode, so I thought I'd bump it up to normal and turn the extra stuff on

Second jump: boarded by five rebels and wrecked

I give up on trying to get the crystal cruiser. I got the stasis pod in my first sector jump, then I got the crystal crewmember in my second one, but I never encountered the rock homeworlds after that.

You can also unlock it by beating the game with every single type A and B ship.

Well yea, but considering I still haven't managed to beat it once since the advanced update, I think that would be even harder, haha.