I think it's the fact that he doesn't see him here long term, combined with the fact he has no resale value.
I've got a sneaky suspicion that he's playing Fellaini more to help keep some of his value (in case of sale) and maybe give him a chance to get into the Belgium squad for the WC. Also Fellaini does whatever Mou asks of him so he's kinda like a teacher's pet and game time is his reward. On the other hand, he told Basti he doesn't need him and the latter decided to sit on his contract (his right, ofc) which is substantial on our wage bill, so there's a bit of sour grapes maybe from Mou about that.
Now the above is complete conjecture, but we can see it's not for footballing reasons. Quality wise there's a pretty big gulf in class and Mou is not an idiot, he can obviously see it.