I'm not sure, when it comes to villain origin stories, storytellers always try and portray them as good guys which takes the edge off. SOmetimes there are evil fuckers who are just like that and always have been. Watching Legend of the Dark Kings A fist of the North star story they tried to portray Rao as some well intentioned good guy. In FOTNS he alway had... morally dubious intentions but it was pretty well known that he could be a cunt most of the time.
Depends on the game.
Star Wars is a good franchise to use villians as main characters, but in most games you want to be CHASING the bad guys, not BEING them. I guess there's a few here and there if I think about it.
It's got to do with how well the villain is being put down. Often in games, villains aren't very well developed, which leaves little room for a story based around them that would be compelling to explore while staying true to the base material. You use Ganondorf as an example, but what do we know about him anyway? He's the only male member of a desert tribe, and being so is entitled to the title of prince. Save for his yearning to control the power of the Triforce, that's all there is about him. I can hardly imagine him being portrayed as a darkskinned, redheared gangly youth, possibly of the timid kind, underdressed in worn shorts, a severe case of acne and a pet pig as his best friend. Well actually that would be cool.
But on what note would such a game end? Would the villain prevail and achieve world dominance, or would the game end with the imminent defeat of evil by some unlikely hero?
I think that trying to do origin stories, or fleshing out characters with little stories other than: I am Evil - people would be let down by the results. You saw the fracas over Metroid Other M, which completely flew over my head.
In video games (and perhaps in other formats as well), the producers don't usually give dimension to the "bad guys" they are just strawmen for the "good guys" to knock over (imagine a film based on "the Libyans!" from Back to the Future). BTTF2 was basically about Biff, which is why it sucked so much -- "Me big dumb rich, slow moving guy, Bwah ha ha ha!". condensed point: most villians don;t have the dimension for their own story.
So to answer your question, yes there certianly should be games about decent villians, particularly for long running or successful franchises. I'd play a smaller game (like Vita) that allowed you to play the role of the lady enemy from Uncharted 3. Maybe give some insight into her motivations, you could play as a younger version of her for the traversal parts, and make it more of a strategy game when she is older, deployinbg her goons.
Online multiplayer also works, imagine playing as Wesker in the tanker scene of RE5, trying to defeat two co-op players on the other sied of the internet.
Wesker would be perfect for a game.
Yes, Ravenprose deserves his own game. 
Archie: The Vile Xboner: The Game.
Ravenprose said:Archie: The Vile Xboner: The Game.
Sounds awesome, I'd buy it day one. It's sales would rival Call of Duty and it'd have a metacritic score of 99 only because your score would keep it from 100.
I liked Wicked when I saw it a few years ago. I liked the complete reversal of roles and how Wendy (and the Wizard) is the villain (sort of). Don't know the equivalent of that in games, nor if it cab be done with success in any franchise.
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Listen to Wu-Tang and watch Kung-Fu
A GAF thread made me think about how Big Boss wasn't always the antagonist in the Metal Gear series. We've explored his past and will probably see his motivations for creating Outer Heaven in the upcoming MGSV. What about other villains? Do they deserve their own game to put their motivations on display?
Ganons origin would be ripe for this kind of treatment. We could see him as a young man who wasn't always greedy for power. Maybe he was betrayed by a close friend. Maybe he absorbed the spirit of Demise. Maybe this desert dweller just hates sand because it's coarse and gets everywhere. He may have been sent on an adventure by a senior Gerudo resident, exploring dungeons, finding secrets.
In your opinion, which villain deserves their story told in their very own game? How should their game and story play out?