Louis van Gaal recognises he offers far more than a 9 and if played up top he might lack the discipline because it's in his nature to help out defensively, he doesn't have the playmaking qualities of a 10 in a 4-2-3-1, I'd prefer Mata or Herrera in that role, I'm not convinced Rooney will perform to his potential when Falcao and RVP are ahead of him.
He could perhaps perform the support striker role in a flat 4-4-2 but we don't play that, in the diamond his tendency to drop will mean he gets in the way of the 10 and also in a flat 4-4-2 he would likely need a more pacey striker which we don't have and even then he might find himself clearing balls outside our area and then by the time he sprints back up the counter is dead.
Louis van Gaal recognises his talent and probably thinks he could bring the best out of him as a box to box midfielder but adjusting to a new position will take time, he has goals in him and the more chances we start to create the more goals he'll start getting from midfield. At this point we now would have goals from a central midfielder in addition to goals from the 10, two 9s and potentially the other central midfielder too.
Retraining to a new position will take time, he has the qualities to be effective however he needs to reduce the errors and I also think he needs to improve his short passing and the weight he puts on passes. His passing range is good, his long passes are good and even his short passes however we are talking about operating in dangerous areas, if you lose the ball then you possibly give the opponent a goal scoring opportunity.
Louis van Gaal probably sees the potential, when you look at Rooney he is complete, it actually makes sense to play him there when you look at his qualities but of course he is not going to instantly retrain to that position but when he does he could be one of the best at it and we all know how hard it is to come by a complete central midfielder these days. Furthermore due to his long shots and finishing he could contribute many goals and arriving late into the box will make him hard to mark, he can pop up in the space to take his shot.
It's probably a long term plan.