Rooney has a striker's mentality. His positioning usually very close to the box or in it (hence his high about of goals and assists). That's all well and good, but the primary function of a no.10 is to be the link man - a third midfielder who takes up positions that all him to receive and distribute the ball to the forwards creatively. He might grab a few goals and assists too.
Rooney's idea of 'distribution' is picking the ball up and moving it to the wing and sprinting into the box waiting for the ball to get quickly whipped in. That's totally understandable too - Rooney has a striker's instincts, he doesn't care about building moves slowly because he wants to be in the box scoring the goal. However, that ends up meaning we are very weak and building moves centrally, and we are also very vulnerable defensively through the middle.
I agree that Rooney has a strikers mentality. After all, he is a striker. I think due to Rooney making it clear he still sees himself as a striker last season, and threatening to leave if he doesn't play there, I think Moyes allowed him to play further up the pitch, which like you said, did unbalance the team, although I think if we played the right players and had more imposing midifelders, we'd be fine. While Rooney didn't play as an out an out number 10 last season, he quite obviously didn't play as an out an out striker neither. We've never really played with a no.10 anyway. We've always had strikers who can drop off into the pockets and start off play - a second striker, if you like.
Having said all of this, this is not to say Rooney can't play the no.10 role. I think because Rooney still sees himself as a striker, he doesn't always like dropping off, but under Sir Alex, part of his frustration come from having to play a lot deeper than he did this season, but he proved he could play there, putting in some good performances against City and Chelsea the season before last.
As for Rooney's distribution, yes, he is known for spraying balls out to the wing and getting into the box. That's the 'United way', especially under SAF anyway. Over the years we've been a team that likes to get it wide and cross it in. How many times has Rooney sprayed it out to Valencia, only to get it back and the edge of the area, resulting in a goal? Scholes also used to ping balls out to the flanks. No point playing all this tiki taka rubbish, sometimes resulting in nothing, if we can be more direct. Look at us against Everton. Great possession, kept it well, nice 5 yard passing, but no end product.
I think if we were to add more energy and drive to our midfield in this Summer, Rooney's 'lack' of positioning for a no.10/second striker would be less apparent. I think because over the years we've struggled with this, some say Rooney's not doing enough, but I think if you were to put Rooney in say City's team last season, people be more appreciative of him.