I know this thing has been a dozen times before, but I'm bored :D
Before I start, yes the ending is different if you play lightside or darkside.
Okay, most people don't like the ending becuase it was cut to short. For instance, I assume that you played lightside becuase you said you liked the ending. Now, did you ever once wonder how the Ebon Hawk got to you, considering you crashed on Malachor 5? People just don't like all the unaswered questions. What happend to your party members? Where is the Exile now? The orginal ending (before the game was cut) was much better. For instance, there was supposed to be another fight where you controlled Atton and I think, took on Sion. Now, even if you lost the fight, you would not have to reload and try again. Atton would simple die. This adds to the climax of the games ending. Another thing is that your party memebers were supposed to help you in the final battle...or try. Mira was supposed to charge in and try to take on Traya herself, but she is "Forced Crushed". Also, Kriea did not always have to become Darth Traya. In the orginal game, Atris could take up that role. So, I guess I really don't hate the ending, I just think the other one would have been much much better.
BTW, have you played KOTOR 1 ?