Nihilus was an anti-character. His only motivation (I hesitate to apply that word to him) was to eat the Force. He's shockingly pointless other than to explain why there are so few Jedi in the game, and to develop Visas Marr's backstory.
Sion... uses the Dark Side to hold his broken body together. I guess he serves some purpose in symbolizing a person that depends entirely on the Force, a balance to someone like Atton Rand who survives by his blaster aim and smarts. But the writers never really make anything of it.
Kreia's aspiration of destroying the Force, or teaching the galaxy that living without the Force can be a good thing, sounds all poetic and unique, but it's unobtainable to her. She's a crazy person with a crazy dream. The galaxy was never in danger from her by the time KotOR 2 happens.
The three villains are retroactively meaningful, but their relevance is already over by the time the Exile even meets them. That's what I mean when I say KotOR 2 was disjointed and thematically confused.