Can you provide some more details? What's your class? Which spells/abilities you're using? Are you missing a lot, or just low initiative?
I honestly don't think I've died on the ship in any of my 6ish playthroughs...
Currently, playing as a Ranger. I had the Gith and Shadowheart on the ship as companions and died quite a few times there until I just started avoiding some battles. Now, I'm lv 2 Ranger with Gale, Shadowheart, and the half-vamp companions on the crash site.
I guess I'm just missing nearly every attack roll and the enemies just have too many HP. I rarely see any "hit chance" greater than 50-60% and I usually miss about 90% of the time even with 50% odds (it's like XCom math for me here).