I'm starting to get the hang of it. Beam energy weapons are insanely overpowered and one of the best ways of dealing with the final boss, mainly because the boss is so huge you can easily hit 4+ rooms in one sweep. Also, the Federation Cruiser with a fully upgraded Artillery Beam cuts the final boss to shreds. Beyond that, a lot of stuff works. Ion weapons are great fun for knocking out systems, especially the Ion Bomb (1 power, 4 Ion damage). Burst Lasers are great as all-rounders, being able to overload shields easily and deal solid damage. Missiles just don't give a fuck about shields. Drones are hillarious to watch in a "I'm not touching you!" kind of way...
The only thing that bugs me is how hard it is to unlock ships. Aside from the Engi ship (get to sector 5) and the Federation cruiser (beat the final boss) all the other ships tend to require somewhat convoluted methods. Namely, you need to get to one of the Homeworld systems, THEN you need to find the right jump point in that system (with no hints or anything, so it's blind luck) and THEN you need to have the correct crew, equipment and ship system setup (which, again, is blind luck). For instance, the Mantis cruiser requires you to have a Mantis crewmember, a Teleporter and an upgraded Medbay. And even if you have all that AND you get to the Mantis Homeworld system you can still easily not find the correct jump point before the rebels catch up to you.
Also, Zoltan crewmembers are too useful compared to everyone else. Ok, you might want a Mantis or two in there to repel boarders, but Engi, Rock, Slug and Human are kinda redundant...
