In my opinion, Nintendo opened the floodgates when they included Cloud, a character with little to no history with Nintendo and appears on one game for Nintendo systems (Kingdom Hearts: Chain of Memories).
Sure you had Snake and Sonic beforehand, but Snake had a longer history with Nintendo, especially in the States, and Sonic is kind of self-explanatory. But Cloud is a third party character that is almost completely separate from Nintendo's history and yet he made it into Smash. I don't think it's that big a stretch to want to include characters from indie games, especially with how much more popular they've gotten since 2014. Plus they have included reference to indie games before; there's a trophy in Brawl for Bit.Trip protagonist.
That said, it is extremely exceptional to get all bent out of shape over a character not making it into a game like Smash Bros, especially since the game's already coming with 70+ characters.