Guess I'm gonna take the opposite side here. Apparently unpopular opinions following:
Smash is, first and foremost, a playable museum of Nintendo history and I'd say, if it's not an important piece of Nintendo history, it doesn't have a place in Smash. I like Snake and miss him, but he didn't particularly belong. The NES games were bad MSX ports, the GBC game was neat but not famous, and Twin Snakes, I'd argue, is pretty irrelevant in comparison. His impact on Nintendo history is a bit too small. I don't like Sonic, but I'll defend his presence in the game: Sonic, though he's Sega's boy, is significant to Nintendo's history because of the Nintendo vs. Sega war that was raging in my childhood. Though he's not Nintendo's property, he's still an important part of Nintendo's history. The Street Fighter series didn't stick with Nintendo for very long, but Street Fighter 2 invented the modern fighter as we know it (and Mario's moveset is a clear off-shoot of Ryu's, just like everything that has to do with fighting games can be traced back to Ryu).
Far as indies go, they're important to Nintendo now just like Miis are, love 'em or hate 'em. Shantae's the best rep for it, I think, since she got her start on the GBC in the first place.
All we really needed was a Square rep of some kind and most of our important bases would've been covered.