The Blue Jay:
(Edit, I'm Dumb didnt include download XD):http://www.mediafire.com/download/l58da07flpi52nz/BlueJay.ftl

I got the hull from steamtex, he posted (and some other amazing hulls i will probably use) it in "The Shipyard" Post, so i assume he's not using/has used it.
Here is a view of the rooms:

The ship comes with 2 1x1 rooms, not connected to the main hull. They are accessible except by enemy teleporters (Pretty nice trap actually XD)
this means that if your shield takes damage you can't upgrade it/repair it, so if its level 3 it will always have 1 level shields unless you take more damage on it. The ship does come with titanium system casing so you may get lucky, in my run i lost it in the first fight but made it to the flagship and beat it twice( by that i mean the first 2 stages)
Features
4 charge lasers
1 human
2 engi
mind control, cloaking, 1 artillery(triple missile) (the second one doesn't fire just for symmetry)
4(yes Four) room med-bay
A fully upgraded pilot system
and yes level 8 engines with, if you man the engines over 50% dodge. (no this is not op, the shield counteracts it, without this losing the shields means gg)
It has 1 extra room(2x2) that can hold anything else and one of the 2x1 rooms can hold a battery
Feel free to criticize, praise, etc.
Bugs/Issues
No miniship(too lazy too do, might make it eventually if i really like the ship)
Normal Double Artillery Weirdness(Upgrading does not work)
[Size=150]Tips![Size=150]
Upgrade Shields and sensors, if you can see when the enemy is firing a shot(Missiles top threat) you can time your cloak
If you get all 4 charge lasers powered, you can fire 8 shots, enough to take out even the flagships shields(weaken them, but much lower level 1-2)
If you get a teleporter, TURN OFF THE ARTILLERY, cause if you don't and the 3 missiles fire and kill your people/destroy the ship, without a clonebay you just lost them.
Edit: Pictures Slightly off, i moved the artillery to the very front so you can add a extra system - thanks to stylesrj!