See thats the problem with the majority of fans. You don't see rooney as a problem, because you only judge Rooney on his own individual performance, and are completely oblivious to the other problems he brings.
So what if hes one of our best players individually? Its the total picture you need to see.
Rooney as a striker: Rooney isn't the lad of 2012 anymore. His play style is completely different. Him as a sole striker? He cannot beat his defender, his shot isn't all that special, he lacks height and speed compared to a "optimal" striker. RvP has that technique, height, shot. In any scenario when both in form, RvP is the far superior lone striker to Rooney.
Rooney as a shadow striker: No problem lets put Rooney as a shadow striker. Here the biggest problem starts. Rooney plays fantastic in this role. But he nearly hugs the other striker creating minimal space. He positions his self so deep that there is a giant gap between midfield and offense. Which gives us the oh so fun 2 man midfield drama where nothing is created and forces us to have 2 wide defensive minded wingers.
Rooney as a 10: Has absolutely horrible positioning for a 10, lacks technique, passing and creates next to 0 for his teammates. And worst of all, he doesn't pass forward, but to the wingers (with a huge
Rooney as a CM: Great work rate, good enough passing, good enough vision, still good rushing forward and his play in general is forward minded. But still he loses so much possession in vulnerable places.
So yeah in every position we either have a better suited player for THE TEAM or suiting the play style. Personally if i had to put Rooney on the paper it would be in a 433 with him as false 9, but we simply lack the offensive threat from our wingers to make this work.
Rooney again, is a fantastic player, has great individual performances and gets the job done. But for the team, other players are just better suited. Our team is far more stable with a 3 man midfield, and with Rooney in an offensive position we lack creativity compared to Mata. Any system which involves Rooney as a striker alongside of someone forces a 2 man midfield and thats just a modern day nightmare.