In short Reggie Fils-Aime (president of Nintendo of America) asked Masahiro Sakurai (the main developer of SSB) asked which he likes better; Sonic or Tails. Sakurai got frustrated qith this question, claiming he had answered it several times. The two got in a fight and Sakurai has threatened to remove Sonic from SSB4 if he doesn't receive an apology.
A petition has begun, but it may not be enough. Let's send our support, eh? But remember, it's more important to stop these two from fighting, than to just get Sonic back in the game. We can't always think of ourselves in times like these.