I think Corypheus started out well. The encounter at Haven is interesting. There he has some personality beyond his later "rrraahh, I'll destroy the world if I don't get what I want" childish temper tantrum. I also like that we are actually gaining power visibly and I *really* like that we're in the offensive for the bigger part of this war.
However, at the end Corypheus descends to the ultra-cheesy stereotype, voiding him of anything interesting he might have been. He's right behind Kai-Leng in my lack of appreciation. As has been the case in Bioware's games rather often, the "interesting antagonist" slot is taken up by secondaries - Calpurnia and Alexius. Florianne wasn't too bad either.
I don't mind the type of antagonist who's more like a force of nature, as long as that comes across convincingly. The archdemon was of that kind, maybe not the best kind, but it never wanted to be more. Corypheus came with the pretense that he could be more but wasn't in the end. I started out thinking that Corypheus didn't have the stature to fill the role of an "Elder One", and Haven's encounter made me think he had potential nonetheless. However, any potential he might've had was was squandered. It is only not a critical factor for my appreciation of the story since he always appeared to be more of a backdrop for more interesting aspects of the story, rather than a character with a convincing role in his own right. He made "build the Inquisition" into a plausible line of actions and provided some, well, fundamental antagonism, even though the way he did that was disappointing.