I *really* think you're overlooking Nihilus' special ties to the Exile... Yes, he may have been a pushover in combat, but plotwise he is a central character, and he scared the living **** out of me when I confronted him... Until the actual fight began, that is
<{POST_SNAPBACK}>
I've completed the game twice, and I'm usually pretty good at unraveling the plot, and I didn't notice any "special" connection between the Exile and Nihilus. We "share" an apprentice, but if he's my long lost brother or something, I missed that dialog line/cutscene. (I don't mind if you tell me what I missed!)
It's not that Nihilus and Scion aren't "important", it's just that they aren't fleshed out very well as characters. Even worse, most of the main plot of the game ignores them. You spend your time trying to find lost jedi, not being bothered by or even mentioning these two figures.
So basically, they strut around in a few cutscenes, you kill them, then you forget them. Even if Scion gets long winded at the end, it's just not enough to call him a real "main villian".