Here's the thing.
Snake has been mentioned by Sakurai as a great addition, so I personally don't see what makes him such an easy character to cut?
Not to mention, if Sakurai thought Snake was received well, then I would ASSUME that he would attempt to get him back, just like he got Sonic. When obtaining the rights to property, it is essentially a contract with Konami that was already fulfilled once before, and could surely be fulfilled again. That being, Sakurai has agreed to include Snake in Smash Wii U/3DS. Once he has agreed, it is legally binding if it is a contract (which is assumably what it is). Therefore, if Sakurai has approached/been approached about it, and he plans on putting Snake in, than Snake is going to be in.
This is simply because Sakurai cannot simply go back on a contract like that. Time constraints have zero affect on third parties, as it would go against the agreement/contract to put them in. he can't agree and then be like, "OH SORRY. OUTTA TIME!"
Either Snake is in, or Snake is out. He isn't going to be cut because of time. It's that simple.