If he has a clear plan in place I know fuck all about it. I've been trying to figure it out myself. Before coaching the Dutch national team he was all about 4-3-3, then because of the lack of quality in their center backs he switched to 3-5-2, now at United it seems like he's settled on the 4-1-2-1-2. I don't mind the formation but like you I can't see the logic in some of the positions.
I think Rooney is at his absolute best playing as a number 10, so at the top of the diamond. However if he's going to play Di Maria there then Rooney shouldn't be a holding midfielder, he should be one of the strikers. He did a fine job the other day, but it seems like his versatility is a hindrance. Falcao or RVP need to be dropped. Everyone is on Falcao for not producing, and rightly so, but RVP has been pretty poor as well. The problem that I see is they both flourished as a single striker, or playing with a creative second striker behind them. I just don't think they can play together. If Rooney was the other striker, dropping into midfield, then one of their goal tallys would surely rise.
I also don't understand the situation with Ander Herrera, who has impressed me in almost every game he's played in this season except for the one bad half he had when he came back from a broken rib. When fully fit, I still think our best front 6 is:
---------------Blind (or Carrick)------------------
-----Di Maria--------------------Herrera----------
----------------------Mata--------------------------
-----------Rooney---------RVP or Falcao-------
Or have Rooney play in the 10 role and bring in James Wilson. That may be harsh on Fellaini, who has played very well this season, but he can certainly be useful as a sub.
The problem is, next season could see another squad turnover. My hope is if we qualify for Champions League and Van Gaal has a full summer to work, we can bring in some quality players. The only definites that will be in the starting 11 next season (based on this season's play) are De Gea, Shaw, Rojo (maybe), Di Maria, and Rooney. That's 6 positions available that they could honestly go either way with. Do they make Falcao's loan permanent? (not at 43 million pounds) Do they extend RVP? I would think bringing in a quality centerback (or two) and a midfielder is the priority but wouldn't be surprised if both Falcao and RVP leave and he brings in another striker (Lacazette would do nicely).
The other thing is he's tinkered with formations so much this year. By my count we've played 3-5-2, 4-1-2-1-2, 4-4-2, 4-2-3-1, and 4-3-3. So I don't really know how he plans on lining up the team for next season if they qualify for the Champions League. Its a pretty interesting time.