"During your first run in with him on his yacht, he says the only reason he's aiding the republic is because the Sith is winning. He wants to restore a balanced galaxy."
That's what your fed on the yacht. Later, he retracts it, when you find out he's a droid intelligence given the impossible order of saving the Republic. Which doesn't answer the question - why is a balanced galaxy, and Malachor V in specific, necesarry for the Republic to survive? Goto promises to explain that when he tells the little floating droid guy to "wait and see" what the exile chooses to do, then never does. Because the game was never finished.
"Your guess is as good as mine."
Exactly. We're forced to speculate because the sequences that were opened weren't closed. It's a novel without an ending.
"I won't ask where they come from anymore than I will ask where did all those orcs come from in random encounters of TOEE when I'm 2 inches away from Homlett."
The difference being, TOEE doesn't start a story thread regarding the origin of those Orcs, then not bother to finish it. I don't give a damn where the six dozen Fallen Jedi on Malachor V came from, because they arent' relevant to the story. Theyr just filler. However, when a story arc in a story-focused game is opened, but never closed, it's reason to compain. Why? Because it's very likely that Obsidian intended to finish what it started, but decided not to later on because it wasn't worth the time. That isn't good enough.
"Given the information available, Bioware would have made KOTOR II into another bland black vs white, good vs evil, light vs. dark, ying vs. yang indiana jones story with predictable heroes and machievallian villains. No thanks. I'll take Obsidian's story over that ANY DAY, despite not being flawless."
Let's take a gander at KOTOR2. Villian wants to destroy the Force, and use you to do it. You like the Force, either because your really evil and want to kill lots of hapless folk or really good and want to save the galaxy. And you certainly don't like being used. So you kill villian. Rich.
"This thread is about making the conclusing that Bioware could have done better than Obsidian given a one year deadline. I say that's wrong. If Bioware made KOTOR II, half the posters here would be complaining about how stupidly "Star wars-like" and how black and white the game is."
It's a game about moral choices and the consequences of those choices. As such, it needs to exaggerate the "black" and the "white," regardless of how "grey" the real world might be. But that isn't relevant here - whats relevant is the fact that this game was not finished. Period. There is plenty of evidence to support that conclusion, much of it contained in the games dialogue files themselves! And it's a damn shame, especially given how much more polished and complete the first one was. KOTOR1 set the expectations high, and Obsidian dropped the ball. Period. Blame development times, blame LA, blame the sun god, or whatever - it doesn't change the fact.