More like Snake confirmed not to return:
http://www.ign.com/articles/2014/03/14/kojima-open-to-snake-returning-in-super-smash-bros-for-wii-u
Some may dispute, but consider the following:
1. Kojima personally is involved with all things Metal Gear. He is privy to all licensing agreements involving Snake.
2. If an agreement had already been made for Snake being in smash 4, Kojima's statements here would be not just misleading but outright lying. He wouldn't outright lie when he could just give "no comment".
3. The game is late in development, and it's way too late to add a character. If Snake isn't already in, he isn't going to be added in at this point. I'm not entirely sure Kojima understands this point (he also apparently tried to get Snake into Melee at the 11th hour), but I think we can all agree on this point regardless.
Put together, I'd say it's thoroughly conclusive that Snake isn't coming back. Someone who definitely would know directly confirmed it. Snake should be added to the list in this topic.
Snake's return was a long shot in the first place looking back, but he was a very well liked character either way so it's a shame to see him go. This also marks the first formerly playable character confirmed not to return, hopefully the start of a very short list.