I'm deep in an obssession with this game.
Started playing 2 days ago, managed my first win last night, still have 2 ships I haven't unlocked yet though. But yeah, I've been playing almost non-stop with all my free time.
As others have already said, killing the final boss is easy if you kill off most of it's crew in the first stage. Basically I won the first time I played a boarding-party strategy to the end. Also I really am starting to believe Burst Lasers in general as well as the 2-shot Heavy Laser are hands down the best "conventional" weapons in the game. Sure, Missiles ignore shields, but burst lasers have no problem stripping away shields and still getting hits in, aren't affected by defense drones(very important for stage 2 of final boss), and to top it all off have a >1.0 DMG:power ratio.
Of course there are a few exceptions(the 2-shot missing weapon is great as it is a good way to eat up defense drone intercepts). But by and large I think Bombs are generally a better use of your missile supply- they allow you to disable key systems and are not stopped by shields or defense drones.
Beams can be great, but are a bit more circumstantial as you need a reliable way to take down shields and keep them down or they do nothing. They rock at dropping Zulton Shields fast through.
Also droids could use some rebalancing. Defense I & hull repair are amazing, attack/beam decent, but boarding drone and anti-personel drone both cost too much power for what they do(or rather too much to justify not just using your own crew/openign airlocks to accomplish the same thing). Defense II also costs a bit too much power,e specially considering it's ability to block lasers can actually be a drawback(since sometimes shooting down a laser shields would have blocked anyway means not shooting down the missile that comes a moment later).