Both are very much supposed to be bogeymen. Saren, especially, and right from the start. There's a reason that Shepard doesn't meet him until Virmire (or, technically, the Council's meeting, but it doesn't totally count). The geth are his hand, and they're bad enough. The true terror of Saren isn't Saren in the physical, but his plans and thoughts and pursuits.
And it's the same for Sovereign. Technically, Sovereign's the first "bad guy" we see, even before Saren, when Joker plays the Eden Prime video while onboard the Normandy. We just don't know anything about it until either Noveria (I think Benezia says something about it) or Feros. And even then, details are far from there. Sovereign isn't supposed to be a fleshed-out villain, as Saren isn't. Bogeymen, and in Sovereign's case, representing the vanguard of something far more terrible and sinister.
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