I always believed if your a 3rd Party Character then you really have to have earn your way into the roster such as being an icon and playing an big part of Nintendo's history, (Bayonetta and Joker are questionable picks, But Bayonetta is almost a 2nd Party Character I guess), But this is Sakurai's game not mine so he calls the shots and at least their bigger than your average indie.
Super Smash Bros is essentially the "Big League's" or "Hall of Fame" when it comes to video games and crossover, I mean look at some of the 3rd Party's impacts and legacy:
Pac-Man: Namcos Mascot, Likely the 1st thing that pops up in your head when you think of the 1980's and help defined that era and the arcade, Along side Mario is the most recognizable video game character in history.
Sonic: Sega's Mascot, The "Blue Blur" brought attitude and speed as he was created as "Mario's Main Rival" when Nintendo and Sega were going at each other's throats during their iconic "Console Wars" of the 1990's.
Ryu: Only 2nd to Mega Man as the face of Capcom and is the most popular and iconic fighting game character in the world, Street Fighter 2 is what really put fighting games in arcades and on the map.
That's "Elite" company right there, Plus there's bigger fish to fry like Banjo-Kazooie, Crash Bandicoot, Rayman and Heihachi.
Part of me also kind of gets annoyed when every once in a while when there is some new hot indie game/flavor of the month game and then the developers and fans think that's enough to warrant them an invitation to the ultimate crossover and biggest stage of them all that is Super Smash Bros.