from what i understood, they added a 3rd ending when the game was originally out as people were upset with the 2 choices, but it still didn't fix the issue with the ending, being that, no matter how evil or good you played, it made no difference. no side quests, no helping, or killing etc would make a difference in the end. you could still pick any of the endings.
you could reply as the renegade, but still do the same blue ending.
this to me was upsetting as it felt that your choices throughout the games should change the final ending. if you've got say a score of 30/100 or less for evil, then you can't do the evil ending. 30 or less for good, you can't do the good ending.
if you saved all your team mates, chose certain paths, it opens the neutral ending etc.