hm so he is "kinda Evil" for using bad methods while at the end he is doing it for the greater good, at least thats what i see in some comments. He is similar to Lelouch then if anyone seen Code Geass sacrifacing people and doing what is necessery to at the end save the world.
You have to remember, as far as the player character's personal story is concerned, Wrathion is only giving these tasks to YOU, and not the millions of other players on both sides of the war.
Wrathion is trying to end the war between the Alliance and Horde, and because of the deep hatreds between both, the only way to do that is support the side that he believes will win. Of course, that would be the Player character's side.
When you have evil voices going in your head for a big amount of time, you would be saying crazy stuff to! That line did confuse me though. Him acting as if he had this giant burden to bear. That...amused me. I didn't believe it though because why should I believe someone who wants to destroy the world.
Okay let's think logic, he's young, very young, he was just "born" and says something like "i want peace, my father was bad but il be good, btw go kill some A/H because i know what's best for you and if you do that il give you some legendary gems which is obviously that a young dragon like me with not that big powers can just craft....."
Nope that's no logic, he is obviously EVIL, he might actually be an avatar of sargeras.
Both factions have the same fundamental goal: to protect Azeroth from total destruction. Although both the Horde and Alliance have varying agendas beyond this goal, they still share the common foundational goal of protecting the land they live in. It's clear that protecting Azeroth is priority #1 for both the Horde and Alliance, as shown by them focusing their individual efforts on killing Ragnaros, Illidan, Kael'thas, Kil'jaeden, Arthas, and Deathwing - and all the global threats in-between.
Therefore, when Wrathion says he "fully supports" both the Horde and the Alliance, it most likely means he supports their fundamental goal of preserving Azeroth as a whole. Although this may be his intention - I think he understands (as previous posters have noted - and I completely agree) that key players on both sides need to be taken out before there is even a small chance for the Horde and Alliance to stand together to fight the oncoming massive threat.
As it stands right now, if the Legion were to reinvade Azeroth at this very moment, I guarantee that Garrosh would make attempts to kill Varian and members of the Alliance in the battlefield as the Legion wipes both sides out.
"Is trouble brewing?"
He's playing Trickster Mentor to the PCs. He's Neutral. On the other hand he would prefer not to die and the Legion, etc. would say otherwise. So he's arming us, testing us, slowly forcing the factions into a position where they can best defeat the Legion, etc.
He doesn't want to destroy the Alliance/Horde. Why ever would he smash such lovely toys.
Blizz said they made him to keep the black dragonflight around as villains after Deathwing died so yeah someday he's gonna be evil. Sadly.
You are now future Jack Noir.
Presently, you are trapped in a single moment, which increasingly feels like an eternity. Your boredom is surpassed only by your all consuming rage and contempt for existence itself.
Wrathion's main goal in 5.1 appears to be "unification". He point it out in Call of the Packmaster about Varian, both of the "kill the commander" quests mention he's impressed with how you've "cobbled together support" to defeat them.
And while people may think "kill Horde/Alliance!" is evil and divisive, his purpose may be more akin to separating the wheat from the chaff to build both a stronger Horde and a stronger Alliance.
And my guess is that when he orders the overthrow of Garrosh, it's because Garrosh is ultimately divisive, not unifying.
He's trying to forge a weapon to defeat an enemy or enemies. Until we know what that enemy or enemies is*, we really can't make judgement as to whether he's Good or Evil.
*Yes, yes, everyone thinks it's the Burning Legion. But what if it's the Titans?
I'm sure a convo like this has come up before, the answer I liked the most from that one was, I don't think Wrathion is evil, but his version of a safe Azeroth could be very different to what we want, or something along those lines.