I'm looking at it less as a collection of strictly gaming icons and more as a collection of different franchises and companies.
Granted, Shantae and Shovel Knight aren't nearly as prominent as the others no matter how you see it, but if you remove them, another character will end up the underdog.
Rayman and Banjo are small fry compared to the gaming icons we have in Smash. Remove the indies and they become the odd ones out.
Remove them and...well, we just have Mario, Sonic, Mega Man, Pac-Man, Ryu, Bomberman, Cloud, and Snake...but half of these characters don't match the notoriety of Mario, Pac-Man, and Sonic at all.
The point is, there's always going to be a character that is less known than others. The more that get added, the more complicated that gets. With 11 characters not owned by Nintendo I think it's acceptable to have a couple indies.