This reply will have some ME1 and ME2 spoilers.
I agree to the degree that Saren was a good villain, and that he contributed much to make the ME1 storyline so darned appealing.
But he was not the main villain, and neither is the Illusive man. That role was intended for, of course, the reapers, and as fair as villains go, they're probably among the most badass I've ever seen in a video game.
A race of sentient machines, the size of massive dreadnaught-class warships, that returns on relativly regular intervals(every 50.000 years or so) in galactic history to wipe out all biological life more complex then a chimp, and having done so for at least 37 million years(that's the earliest codex referance I could find of a planet with signs of reaper-bombardment), which means they've eradicated most living things in the galaxy at least 740 times. I cant find any other villain-concept in any games history, at least that I've played, that can even remotely compete with that.
Not only do these cycles stand as an explenation as to why any races havent gone hyper-hyper-hyper technologicly advanced(really, that's one of the best things with the whole deal), but it delivers an act of absolute hopelessness before ME3. And that is to me one of the main contributing reasons why I look forward to ME3 so much: Bioware has delivered a villain that by all reason and logic cant be beaten. The hologram on Ilos may have said "Reapers are not invinsible, if Sovereign faced the united fleets of the galaxys races he'd be buggered", but a fleet of them? Thousands of Sovereigns?(or slightly smaller and weaker versions of said ship, since it stands to reason Sov. as a vanguard was fairly badass for a reaper)
It delivers an exciting question that is way better then having Saren or the Illusive man or any humanoid as a main villain:
How the fuck can Shepard win this?
Finding that out will be very interesting. At least I hope so.
I dont think the Ilusive man is as good a villain as Saren, but he's by no means a bad one. They both pale in comparison to the reapers though, as they are perhaps the most mysterious villains of all. We know what they plan to do, somewhat(same thing they've done for millions of years), we know they are really really really tough opponents and we know they can play with peoples heads.
That's about it. We dont know why they do it, we dont know how old they are, we dont know where they're from, we dont even know if these are the only reapers. There are a ton of questions unanswered by these behemoth villains, and just because they dont have human faces doesnt make them poor villains.
I guess I dont feel the same need to have a human/humanoid face to everything. To me not being able to identify myself with the villain just makes them more mysterious. Who the hell are these guys? What can they do? What are they after?
I just cant say that a race of villains that are a mix between skynet and cthulhu are anything but badass.
Of course, the easiest way Bioware could sink all of my fanboyish expecations and excitements is if Shepard just gathers a fleet of a few thousand allied ships and defeat the reaper fleet in orbit, and that's it, game over, grats. But that would violate all manner of sense and reason behind building such a formidable enemy, and I have faith that something special will be required to achieve victory.