One of the big flaws with KOTOR 2 is that it doesn't make the player care that much about many of the bosses you fight in the game. Like when I killed Nihilus and Sion, I didn't really feel like I cared that much, tbh... simply because these characters appeared so little in the story in a way that touched the main character in a dramatic way. Sion, I suppose, appeared a few times early on... But otherwise, not really.

I suppose you could point out the Sith minions attacking the Jedi throughout the game which ultimately would have been directed by Nihilus, and you could point out the exchange bounty hunters going after the Jedi, which ultimately (probably) would have been paid by Nihilus, but the relationship between Nihilus and me the player never really made me despise Nihilus and want to wipe him out, which I consider problematic simply because it makes the ending less satisfying when you eventually wipe him out.

What they did with Kreia was a lot better because Kreia touched the life of the main character so much more than Nihilus or Sion, which made the ending more satisfying, meaningful, and intriguing because it related to the experiences of the main character in the game much more directly than was the case with other bosses like Nihilus and Sion.

Essentially, I'm saying the game could have been improved upon if it made me hate Nihilus and Sion more. Or at least care more about wiping them out.

I agree with you. Nihilus and Sion have too less screentime in the game.
Kreia is imo the best of them especially her motivation is far more complex than just conquer the Galaxy.