Couple of average games? I imagine you're forgetting his and Nani's horror show at home to Galati? I was quite frankly disgusted by the way those two played. I can accept that players will have poor games, but neither of those two looked like they even wanted to play. Giving the ball away constantly and needlessly, and not getting out of second gear is inexcusable. It's that attitude that sent us out the Champions League.
You say he's a pretty good player, I wouldn't disagree, though I don't think I'd class him as any better than "pretty good", but that seems to suggest that if Rooney was a midfielder, he'd be worse than a "pretty good" player? Personally I disagree, and think he'd still make a very good footballer, albeit with some obvious weaknesses.
If we're talking about Wigan at home, I think I'd play Rooney. It's similar to the Rafael argument. Why play more defensive-minded players when it's not necessary? Realistically, how much of a threat are Wigan going to pose? Personally I think a midfielder, two centre backs, and two wing backs would do the job comfortably.
If you ask me, would you rather leave Rooney on the bench, rather than play him in midfield ahead of Anderson, I'd say absolutely not, get him playing.