LvG loves anyone who follows his instructions and I think the simple explanation here is that he likes Valencia's conservatism. He's very prudent in his overlapping runs and in his use of the ball (I imagine that exactly what LvG wants is for him to turn back and play the ball back infield if there's not a great option on). I think all LvG wants from the full back is to back up the play conservatively and play the percentage ball to Fellaini at the back post, or otherwise recycle possession. Valencia does that to a tee, and will do it 90 minutes no problem, whereas that's not Rafael's natural game.
I was basically going to say the same thing here. I believe van Gaal sees Rafael as too adventurous for the 4-3-3 with the point back in which the central midfielders tend to push higher up the pitch than in a 4-2-3-1/4-3-3 with the point forward. When van Gaal played his 4-3-3/3-4-3 diamond with Ajax, he had Reiziger and Frank de Boer as full backs. With Barcelona, he had Barjuan/de Boer and Reiziger. With Rafael being more adventurous going forward than Valencia, van Gaal will always opt for Valencia's safer, more conservative style. Even Herrera and Mata still have to fully adjust to Valencia's conservatism (notice the few passes they play forward with Valencia not even making a run into the space).
I'm sure that, at the moment, Rafael is currently not playing as he's probably too adventurous with his runs and positions for van Gaal in this formation. If we were to play a 4-2-3-1/4-3-3 with the point forward, I'll have no doubts that he'd play Rafael over Valencia. When Rafael was fit, he'd be playing in the diamond setup ahead of Valencia. It was only when he got injured that he was taken out of the scene. Since then, van Gaal won't shift out Valencia unless Rafael pretty much becomes as conservative as, if not more, than Valencia going forward.
Defensively, I still think Rafael's better, but going forward, I believe Rafael isn't conservative enough, yet. However, I'm sure van Gaal will change Rafael's game so that he can suit the classic 4-3-3 better, just like he did to Herrera.
Judging a FB by goals and assists is pretty silly.
To be fair, ever since Dani Alves and Maicon came into the scene with their ultra-attacking style, football fans now expect full backs to be more productive. Still, though, you don't really see many full backs be that productive, judging full backs solely by their goals & assists isn't the best barometer for a full back's attacking output.