To answer, Shadow Moses Island seems the most likely. I love that stage, and if it comes with new music, Heaven's divide would be my number 1 choice.
Anyway, I feel like talking about Snake's chances right now. After recent events, it seems to be getting just a bit better.
- He's relevant (Obviously)
- He's a popular choice
- Kojima and Konami may be a bit of a problem, though I don't think it greatly affects his chances.
- He has a unique movesets that no one has been able to replicate.
- Nintendo has reached out to Konami to make a Hudson Soft game. While it may not effect other Konami IP's, Nintendo still thinks its worth reaching out towards Konami for negotiations.
- This is something more related to Nintendo, but it was recently said by a Nintendo Treehouse employee, that they have other game consoles at the headquarters for employees to play and have knowledge on other games. It was something that reinforced the idea that Nintendo doesn't care for competition, and more on fun. And considering how people like to say Snake was on other consoles more, it seems Nintendo doesn't care for that (Look at Ryu who's appearing on other consoles more). If Sakurai were to pick a 3rd party character, it would most likely be based on legacy, them actually appearing on a Nintendo console, and the support for said character.
I would say Snake is in pretty good shape.