Disclaimer: While I am Biased for Snake to return, my only goal in this essay is to try and shead some light on the facts and help develop peoples arguments.
Snake's return in Smash is one of the most debated topics about the game. As with any debate, there are two sides to this argument.
Pro Snake Side:
-Snake is a unique character
-Snake is popular among smashers
-Snake is a Smash Icon
-Snake will return unless Sakurai and/or Kojima says so
Anti Snake Side:
-Snake isn't a Nintendo Character
-Snake is out of place
-Snake advertises for the competition
From what I've read, the anti side seems to making a more logical argument. However, one thing I think they have failed to noticed is that their argument could be the very reason why snake returns.
SSBB was released before the release of MGS4, so the MGS franchise within Smash contained multiple element from all of their games, but most predominantly the yet-to-be released MGS4 (ex. Gekko appearing on Shadow Moses). So nevertheless Konami was advertising through Smash, and Snake became a popular character, not just because of his competitive viability, but because of his unique and entertaining play style. As gamers like myself played the character, they got attached to him and wanted to know more about him. They would look him up, and learn not just about Snake, but the whole MGS Franchise. And MGS is one of the best series of games I have ever played. It one of those games were once you pick it up, you can't put it back down.
However the opposite is also true. Snake also appeals to gamers who already like MGS beforehand, and they might start taking an interest in Smash, and may lead them to get addicted to all the other games franchises within, such as the Legend of Zelda or Metroid. This in turn generates profit for Nintendo.
So now we have a a group of gamers who not only love Smash, but also MGS. An as Eddybear asked earlier in this thread (Page 4, post #136) "If Snake wasn't included, would it be a dealbreaker for buying SSB4 for you?" These Smash/MGS fans now have to ask themselves, "Do I want to buy this $60 Smash game when I can just download Project M?" and potentially a $300 Wii U? (Let's face it, the Wii U isn't doing so hot right now).
So Nintendo now has to choices
1.) Advertise Snake and MGS and appeal to a good chunk of gamers who might not otherwise take interest in their games, but risk upping sales of their competition.
2.) Cut Snake and MGS and lose appeal to a chunk of gamers, but prevent advertising for our competition.
Snake's fate in SSB4 depends on a multitude of factors, such as what Nintendo sees on the most profitable decision and if there's enough push from the fans, but in the end, it is Sakurai's decision.
It should be clear there is a pattern to it but if people haven't realize this then it is just very sad. 
