The thing that really made TFTD annoying was the Lobstermen since you couldn't just lazily grenade them into oblivion; blaster bombs and MC still made a joke of the game though if you permitted yourself to abuse them. I did manage to win on SH Ironman with the alien weapon self-destruct and without using MC or BBs. T'Leth was tense because you had to be _very_ careful to avoid getting blaster bombed (i.e. have a door or other obstacle between yourself and a trajectory).
Cruiser needs some weapon bay areas with the glowy plasma tanks (it kind of has one, it just looks like shit), a briefing area, proper bridge, medbay (stasis chambers and surgery would do for this), food/life support module, storage facility, and living quarters, maybe even a brig.