It wouldn't surprise me (or disappoint me) if Corypheus was acting on behalf of or for benefit of the Old Gods.
Though I'm also certain Flemeth will play some major role in it all, too, and Corypheus could still simply be a major but not the final villain.
This is what I'm thinking as well.
Having Corypheus being one of the bosses/baddies behind the Veil tear I can buy, but being the mastermind behind the whole plan and being the ultimate villain of the DA:I ... not so sure about that.
He was an interesting character and boss in Legacy, but I feel like he's a bit too "been there, done that" to be the final final boss. Most probably he's working for either the Old Gods, or possibly one of the Forbidden Ones (since all of the Forbidden ones have made an apperance in the games/books except the Formless One, who is still my guess at the moment). And Flemeth is always a possibility, although I have a feeling she's more interested in self-peservation than world-domination, though I could be completely wrong about her and her motives. In any case, I think it has been confirmed (?) that she's at least making an appearance, so my guess is that she's in some way involved with either the Rifts or the Inuisition -- or both.
Then there's also the possibility that Corypheus is the ultimate boss of DA:I, but the game ends with another cliff-hanger and an allusion to the (wo)man behind the curtain.
But to make Corypheus a compelling villain for the whole game there would have to be loads of new stuff for us to learn and to discover about him so that he'll make sence as a threat - Hawke and co. gave him a pretty good whooping (or at least it looked like they did) in Legacy, and in my opinion there needs to be a good enough explanation as to why he a) didn't blow a nice little hole where the Vimmark Mountains used to be and take Hawke and co. plus the Wardens out completely, or
: did the song and dance with Hawke if he's able to pull Fade Rifts out of his robes whenever he pleases.
But it appears he is one of the ancient magisters who have teared the Veil once already... maybe the Real Big Bad came for him (and the other ancient magisters) for help to open the Rift as a part of his/her Grand End Game Plan?
But all in all, not really convinced that Corypheus is the Final Boss. But if he is... then I'm glad I got myself accidentally spoiled, because at least now I can brace myself for the disappointment.