Yeah...I had a hard time understanding parts of the ending as well(...first the Ebon Hawk, all banged up, falls into the chasm - then, fully repaired, it picks you up?!...Just to mention one thing).
It really feels like a rush-job, and that's sad as the game was nice otherwise (aside from the crashing when loading about 1/hour, graphics glitches etc.). I suppose this just goes to show that good and immersive stories can make up for a lot of cr*p, eh?
It is my hope, however, that Obsidian and Lucasarts have gone for a "Empire stikes back" -type of thing, where matters are left purposefully unresolved just to be wrapped up in the finale (KotOR 3).
I guess I'm just an eternal optimist