Deathwing and Arthas are not really under that catagory... You have to see greater good in a whole different perspective.
I think that Wrathion can be a villan, but also a good guy. The last scene in MoP ends with him being scoulded by the bartender who tells him that it is the hardships and fights that we go through in life, that have made us strong. The horde and the alliance have survived through the previous dangers because they constantly had to go up against each other and try to become more powerfull.
What if Wrathion, while he pushed it away at first, took this very litterally? Maybe the whole WoD thing was a win-win situation for him. Either the Iron Horde would take over Azeroth and be powerful enough to defeat the Legion or the Horde/Alliance would win and become stronger through their fight with the Iron Horde. Ofcourse he could not have known that his actions with timetravel would create the burning legions invasion of Azeroth, but from a standpoint of being the protector of Azeroth, he did pretty well.
Anyway, for him to a future villian, there has to be a reason for him to attack us or for us to attack him, and so far nothing has really been lost from our time in WoD and we are doing things he like atm.
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Well he did leave with quite a bang, so why would he be hiding? Only the adventures know of his "failed" plan to create a stronger union on Azeroth and nothing was wasted. He got what he wanted mostly, since he gained a mogu heart infused with the power of a titan and the blessing of the August Celestials. He won alot in MoP and lost very little.