When you get right down to it, there really aren't any big "villains" in Mass Effect. Antagonists, sure, but nobody is doing anything terrible just for the sake of being evil or even for self interest. And I'm fine with that.
Saren may have been a dangerous arsehole even before he was a reaper puppet, but most of what he does is for the greater good as he sees it. Same goes for Benezia, the Shadow Broker and TIM, more or less. The Collectors were just highly developed husks under reaper control. The Reapers themselves are little more than tools and extensions of the catalyst, which is just fulfilling it's function in the best way it knows how. Even the Leviathans that created it were acting out of concern for their thralls and were simply the victims of their own hubris.
Actually, the closest thing the game has to a villain is Wreave, and he's technically an ally!