Of course Snake has his fan base and is popular. I've played one of his games. The thing is, he wouldn't be that popular in
Smash if he were bottom tier. Most MGS fans don't play Smash. Remember why Mewtwo got cut?
As far as how likely he is to actually come back, yes, I'd be surprised if he didn't. Due to his popularity he'll come back no matter how undeserving he is. If Sakurai directs SSB4, that makes Snake a complete lock of a returning character, seeing as he put him in Brawl based on a personal whim (The request of Snake's creator who's name escapes me. Kojima or something).
Scorpion isn't important and doesn't have people asking for him in the Smash Bros. community. No chance. Just because a 3rd party character can get in doesn't mean everyone and their grandmother can get in.
Oh, almost forgot.