Snake of course made his series debut in Super Smash Bros. Brawl for the Nintendo Wii. His addition to the game came as a shock, being the first third party character to appear in the Smash Bros. series at that time before being joined by Sonic the Hedgehog.
In the interview Kojima expressed that it was not likely that Snake would be returning to Smash and that ultimately the decision will be left to the director of the game, Masahiro Sakurai. That being said, Kojima did note that he really wanted his character to make a return.
"I'm not working on that game, but i don't think it's likely. If Mr. Sakurai is watching this, hopefully we see Snake."
The Metal Gear series, despite being third party, has plenty of history with Nintendo. The first Metal Gear game was ported onto the Nintendo Entertainment System and as recently as 2012 we have seen Snake grace a Nintendo console in Metal Gear Solid: Snake Eater 3D for the 3DS.
With yet another third party addition being added to the roster in Mega Man and numerous characters that were thought to be cut, such as Toon Link, making a return, it appears that Snake could still have a chance to rejoin the fight. Like Kojima said, it will come down to the preferences of Sakurai in the end.