He's happy playing as a second striker I think. Last season he was playing off the midfield more than he was the attack, and a number of times was just in midfield. It was a noticably deeper role than he'd been asked to play in the previous seasons and he looked uninterested in fulfilling it.
Kagawa hasn't done "more than fine" all that often at all. I think he's been decent in some games, but even then the general consensus from fans tended to be less complementary than mine. He hasn't done anything to suggest he's worth dropping or shunting Rooney around for.
Rooney's been playing further up, but he's still playing off Van Persie. One of the big frustrations of last season was seeing us lump balls into the bx for Van Persie to try and win on his own against 3 or 4 defenders, so it's not the dumbest thing to try. Both also have a good goal return this season.
The games we've played worst in, it's been our defence and defensive/base midfield play that's been awful. We've had horrible problems with playing the ball out from the back and winning back possession before it's inside our penalty area, as well as basic duties like marking the only opposition player in the box. You can play Rooney as deep as you like, he's not going to help any of these things. Neither will playing Kagawa instead of him, regardless of how well Kagawa might play. Also, two of our worst performances involved Rooney and Van Persie not playing together anyway. While our better performances have been with them both on the pitch.