Exactly, and it is pretty terrible to see this. Because of Fellaini I kept on thinking how our team of yesterday would compare to Everton when Moyes was coach there. We were trying really hard which was great to see, but there was not enough quality. As for tactics, Van Gaal is very much a coach who wants to build from the back, and in the end he's responsible. But he can coach all he wants, if the players can't apply it then it's useless. So I don't know how much you can realistically blame him, but if he can't fix it there's no excuse.
But I also saw Mata has played in 25 matches this season, Fellaini in 21 matches. Don't know about minutes, but I do know Mata almost always plays as a #10. Van Gaal probably quite likes Mata, maybe not as the ideal long term #10 but in this squad it's a player he normally likes. But he sees it just doesn't work and tries something different with Fellaini, because first the defense, and then like you mentioned also the midfield struggle with their decision making on the ball so long balls will be likely to happen.