I'm actually starting to think it was business issues that kept Snake out to be honest. First there's voice actor changes, due to certain ones passing away (Colonel's Japanese VA passing away) and one's being replaced (David Hayter as Snake). Then you have to think about the codec's being brought back or not, them agreeing on Snake having is Brawl design or his MGS4 design, stages, and hell, if it was indeed a problem, his moveset (One that I don't and will never agree on, but will accept if the case). Snake is a sad case indeed. And I just went back and played as him in Brawl (and PM), and oh my God is he so much fun to play as.
If he gets the chance, I really hope they revise his chances as DLC...