I think the idea of Snake being cut is a complete myth perpetuated by Smash spectators only. That's how you can tell if a rumor is fake, especially if they say "he's on the chopping block due to rights issues."
In E3 Sakurai said there were no cuts at the time, meaning that Snake was still intended to be included at that time. If there was an issue with Konami, he would have been cut immediately. He's either in or out. There's no maybe.
His statement would imply that cuts would only be made for the sake of time or technical limitations. If they already jumped through the hoops to get and keep Snake, I doubt he'd be the first one to go. So honestly, I disregard any rumor that says Snake is cut (at this point, I'm starting to discredit rumors with any cuts).
Clamoring for cuts stems from Smash speculators' love of "muh patterns!" They are so obsessed with this idea that they forget that Brawl didn't have a single trash, throwaway character. Melee did, and in addition to Mewtwo, those were the ones that were cut. And we can see from the Brawl files that Mewtwo almost made it in.
If Sakurai really gets the enormous amount of development time that we think he'll get (and has already had, honestly) without wasting 60% of it on a single player mode, in addition to not having to build the engine and models from scratch, I'm having difficulty seeing why there needs to be any cuts.
Then again, you never know with Sakurai. Regardless, keep this in mind.