Saying the "New" Black Dragon Flight is evil, is like saying Republicans are evil.. .. Wait a minute. bad example. (jking, not all, just the crazies)

Black Dragon Flight! Now under new management!

Making him evil would negate all of the build up of repairing all of the five flights to their glory in the Thrall: Twilight of the Aspects book. We also need all five together to kill Chromatus, in some future instance. Black Dragons are characterized as highly analytical and pragmatic. We need one of them on our side considering the monstrosities that are left to deal with. He may not be evil, but that doesn't mean he's very nice, considering the state of the planet.

Wait, I got his secret plot:

It's to steal the power of the Old Gods without being corrupted like Deathwing.

Assuming Wrathion wants to save the planet, he knows he can't deal directly with the Old Gods or history will repeat itself, he's got to send a proxy to deal with the Old Gods. That's where the rogue comes in as Wrathion's pawn. Wrathion recruits rogues who see the big picture, who are willing to get their hands dirty to ensure an Old-God-less Azeroth for our new Earthwarder.

The mission for the rogue is to extract N'Zoth from Deathwing, and have the daggers become the host and cage for the Old God in order to use its powers for our end. Wrathion will use the daggers to study N'Zoth and find a way to counter its corruption like the Titan construct was able to purify his own corruption. Such a plan would be insane enough that most classes would be correct in saying "no", but rogues, they are willing and able to go down that road to ensure the future of themselves, or their faction. Black Dragons being pragmatic will handily explain why every rogue can start the quest: he's going to throw away a lot of weak and useless rogues in order to find the one who can succeed.

I sort of want this to be the case, so that at the end of the quest line, Wrathion as the new Earthwarder with a caged Old God under his thumb will put on the greatest "JUST AS PLANNED" face and gloating over the remnants of the Black Dragonflight and commanding them to submit under him to serve the world once more. Such an ending would be a character introduction beyond badass.

The comments from interviews on the subject a week ago were not promising either. I hope it turns out awesome, despite the fear....