I don't see what isn't fitting about him.
He's a third party character. He isn't owned by Sony like a lot of people tend to try and say. Sure, a lot of his content in Sony oriented, but it's not like Snake has ZERO history with Nintendo.
Solid Snake is a goofy character. He isn't a Master Chief. He hides in a freaking box to avoid detection. If you have any knowledge of Snake and MGS as a series, then it's not at all weird for Snake to be silly looking as he runs around and smacks people with his legs.
While I could understand him getting cut, I would certainly be upset about it. People forget something very important.
Solid Snake was the FIRST 3rd Party character in Super Smash Bros. Not Sonic. Not Mega Man. It was Solid Snake.
Snake has become a very important part of Smash Bros. history. Maybe he got in because of a favor, but he meets Sakurai's criteria for Smash Bros. He is legendary, and he has appeared on Nintendo platforms. So yes, he fits.
Even if some fans don't think he fits, or has little relevance to Nintendo, Sakurai
clearly disagrees. He had trophies and content from Metal Gear Solid IV, a game that has never been on a Nintendo product. Yet, Sakurai included it anyway. So the fact that Metal Gear Solid V is in the same boat is irrelevant.
The graphic style won't fit Snake? Snake has been in HD for years now. Oh but it's colorful? Who says Snake can't be colorful?
I'm not trying to be an ******* here, but most Snake arguments I've seen are butthurt Nintendo purists who don't think it's fair for Snake to be in. Snake isn't Master Chief. Snake is a legendary 3rd party character, who isn't owned by a competitors company. So no, it isn't directly supporting Sony or Microsoft. It's supporting Konami, just like Sonic is Sega, and Mega Man is Capcom.
Snake's my home boy. Come at me