Van Gaal is doing what Moyes didn't have the capability to do which is actually finding a system to suit his players. I think he's done well, but personally I don't see 3 at the back working in the PL. Most teams will set up with 1 striker against him and camp in their own area which negates any of the advantages. Add to that the fact that it's hard to get an overload down the wings unless someone pulls out of position, and the fact that it's easy for the opponent to overload your flanks forcing one of your players to come out of position, means it's an easy formation to exploit. At the end of the day, football formation is about covering the whole pitch in the best way and two at the back is more efficient than 3. It was only really useful as a counter to the 4-4-2 and I don't see many teams lining up like that, especially against Man U. I would have preferred a 4-4-2 diamond like Rodgers last season if I wanted to fit two strikers in.
On the other hand, I'd love to see a smaller team use 3-4-3 to take Man City apart when they have the cheek to play 4-4-2.