Samus, Zelda and so on are more or less fictional comic characters / heroes. Snake more or less is just an ordinary human i.e. agent - a fictional figure too though he's taken right from "our real universe" and this is what I don't like about it...

I mean it doesn't fit to the rest in my opinion and even worse including him opens the gates for pretty much anybode else - so we're going to see Gordon Freeman, Sam Fisher, a character from Warcraft or Unreal Tournament too because well they fit into the same category as Snake. Super Smash Brothers is about fun fighting with cool comic characters. And I say it again - imo a character like Snake doesn't fit in there...

He won't ruin the game of course but when I think of Sonic fighting Snake - that just doesen't feel right...

Enjoy your meal
Toast