Top 5 Reasons I think Snake will be back:
1. Metal Gear's creator asked Sakurai to use him.
2. He was a unique and very special addition to Brawl and was quickly one of the most loved characters in the game adding a whole new genre to the mix. No stages in the game felt quite like his, with the epic espionage music and the snowy night. He'd be backtracking to get rid of a character who adds a cool new element to the game.
3. Sakurai loves doing things to make his fans happy and he has an eagle eye on the things we talk about. Example: Remember when he announced Waluigi? He said "Just because you try hard doesn't mean you'll make it in." He knows that people requested him and talked about him a lot. Remember when he announced Lucario's Mega Evolution being part of the game? He made some sort of reference to making fans happy. He knows what we want and will do what it takes to make it happen.
4. Project M: With Project M always updating their brilliant game with new costumes or stages, I'm certain Sakurai feels at least somewhat threatened by them. I'll bet you he wants the Wii U version of Smash Bros to replace Project M at tournaments, and by limiting the selection of popular characters, he'll be lowering his chances of being successful in this endeavor. (This is also why I think Roy will be a Lucina alternate, and Mewtwo will return.)
5. Because there is literally not one good reason to cut him. Snake was an odd choice for Brawl and he fit in (surprisingly) perfectly! You don't fix what ain't broke! Smash bros would just feel like something is missing without Snake.