Why would you take Rooney deeper, further away from goal, when you're deliberately trying to score? Nobody here is implying that Kagawa should be played at CM against City, rather that if you're playing against West Ham or someone next year and they're sitting deep, having someone to break from deep in midfield can help create an overload in specific areas of the pitch.
That I have said also, if we are playing lesser teams Kagawa can play as anyways he will occupy AM as we dont need to defend. But against any decent team we can't.