The business model that Smash was supposed to be was having people who are Nintendo oriented in the game. I'll agree that Mr Game and Watch & Rob had more desire able move sets, but they still feel more welcome then snake to me. Snake would have been more at home with Playstation All Stars, without having to resort to dumbing him down to fit. Sonic and Mega Man may not be Nintendo mascots, but they have been associated more with the company besides early Metal Gear.
I wouldn't cry if Snake returned, just upset they wasted a 3rd party slot for somebody not too many people wanted. Then again, I'm fully supportive of team Geno so I may be biased.