The thing is, Bioware did a lot of good with Corypheus. He was a constant - albeit in the background. Unlike DA:O, we had an actual antagonist we took steps to thwart. He was - via In Your Heart Shall Burn (and IMO potentially In Hushed Whispers) - introduced in an absolutely phenomenal fashion.
We just needed more confrontation. I thought Virmire did a lot wrong in ME1, but one thing it did right was (1) feature a Saren/Shepard showdown where (2) both Shepard and Saren came off bloodied.
We need more confrontations with the Big Bad throughout the game, where we trade blows.
I think this is part of it. The other part is that we need to lose to Cory at least once. And lose big time. Not like In Your Heart.... where, to all intents and purposes, the Inquisition won a strategic victory - they closed the breach, destroyed a significant portion of Cory's forces and managed to withdraw the bulk of their people including the entire leadership despite being attacked by overwhelming force. Even more than the lack of direct confrontation, the fact that whenever you go up against Cory or his forces, you win, or at the very least, you disrupt his plans (e.g. at the conclave), really takes away from him as a creditable antagonist. By the finale, killing him felt more like putting him out of his misery instead of defeating a huge threat. And that was such a let down to me, as I think Cory had so much potential be to a great villain, based on his character and story, and indeed, as you point out, his initial introduction.
Having him really defeat you at least once builds him up as a credible threat far more. And it makes thing more personal. You want to get him back. You want revenge. Both of which are central to creating great villains IMO.
For me, Bioware's two best antagonists by a country mile are Irenicus and Sun Li. And both of them have this kind of moment when they triumph over you - for Irenicus, it's him taking your soul. For Sun Li, it's him killing you and taking the throne. Cory never has anything even close to those events.
The closest is the Haven part of In Your Heart Shall Burn, as he certainly does damage to you, but even then, look at how it ended. You outsmart Cory, taking advantage of his arrogance to release the trebuchet and trigger an avalanche. That scene leaves the Inquisitor looking good and the big bad, for all that his introduction over the previous minutes was excellent, looking stupid. Straight away, he's immediately made to appear significantly less threatening. I would've had no problem with his arrogance casuing him to let you live after beating you (e.g. he tosses you aside after failing to take the anchor back and you are able to escape), but for the big bad to lose to you mere minutes after his introduction makes him look weak. And for an antagonist of the world threatening type like Cory, that's pretty much the worst thing you can do.