Behind everything will be someone we have seen a connection to. It may not be Corypheus, but it could be someone as yet unidentified connected to him. It's not going to be completely new player with no previous introduction. I'm guessing someone from Origins for the simple reason of "If you show a gun in Act One, you need to fire it by Act Three). Inquisition looks like a big ol' gun is being fired.
It's also not going to be a moustache-twirling villain who only lives for Chaos. Despite what Alfred said, people who just want to watch the world burn make for terrible plot. Even of it looks that way at first glance, there will be a bigger picture revealed later.
I don't believe it's Flemeth simply because she seems to be in it only for herself, and she gains little to nothing from these events.
I'm of the personal opinion that the rip in the Veil is a distraction. A huge one mind you, and it may serve another purpose ultimately. But ripping open the veil doesn't seem to be a big enough goal in and of itself. that said, *a* reason for it could simply be the "fade spirits are jealous of humanity." Justice was really getting seduced by the experience of being human.
But what's bigger than that? Where is the dramatic tension on a character level? The big reveal will be a twist of some sort (possibly even a twist on a twist) and will have a deeply rooted character motivation at its heart. One of the only ones I'm coming up with is tied directly to the original magisters.
It's not just to be evil, but destroying the Maker's creation is a huge middle finger for the perceived damnation they suffered. They're going to think the punishment was far too severe for their crime. The prideful never think their arrogance is misplaced.
The OGs seem too foundation level to be responsible, though Flemeth being an uncorrupted OG isn't too far fetched. And of course, Morrigan and the OG Baby will probably be significantly involved in the resolution of the Flemeth plotline. Morrigan turning Flemeth's plan against her, even as Flemeth thinks Morrigan is dancing on her strings, would be great. It's a version of the "I know that you know that I know" deal.
Back to the mastermind though. I just had a thought while typing all this. having a mortal human ultimately be behind all of this, a chantry person for example, would be a dramatic coup. Think of it - if you're a devout, true believer who wonders why the Maker could have abandoned everything just because of the Magisters, what would be a way to get his attention? Do everything you can to put the world in jeapordy - force the Maker's hand. If a mortal could have manipulated these things, set forces in motion simply to get Dad to show he still cares... AND if you can pull it off believeably, that would be strong.
So now I'm going with that. The ultimate string puller is a mortal who wants god to come back and fix everything and love his children again. If anyone could undo all of this and turn Thedas into a paradise, it'd be the Maker.
(I'm not saying the Maker will show up or anything, just that, in this hypothesis, that could be the reason behind the crazy.)