Loving this and finding it quite addictive. Managed to unlock the Zoltan, Engi, Rock, Federation Cruiser and Kestrel layout B so far. Easiest way Ive found to having more scrap than i can even use is killing all the crew of the other ship without damaging (or as near no damage at all) to the hull, this ends up giving you really good rewards (i find i get a lot more free weapons or augmentations this way). To do it you'll either need anti-bio weapons, teleporter, ion blaster or bombs (or a combination of them).
Furthermore the final boss doesn't re spawn crew between phases, which means if you can perma tank him on phase one (quite easy with 4 shields, defense drone I and decent evasion) you just teleport your crew into the 4 gun rooms (not connected to the rest of the ship meaning you wont get swarmed) destroy them and its crew, and then focus on the rest of the ships crew. This means you can just teleport your guys straight into the drone room on phase 2 and have no problem destroying it and they cant repair it.