Greninja.
Since the beginning, the central idea behind Smash was bringing together a cast of Nintendo's biggest All-Stars and letting them fight each other in massive free-for-alls. It was he chance to see gaming legends like Mario, Link, and Pikachu face off. Now, the definition of "All-Star" has certainly been stretched ever since even the first game in the series, with the inclusion of characters like Ness, Ice Climbers, Lucario, etc. The series hasn't shied away from including more obscure or minor characters alongside gaming giants, and I can accept that; most of the characters included could at least claim to have some significance in the grand scheme of things, and had made a name for themselves prior to being playable.
Greninja, though... Greninja was added to the roster when he was still being developed as a character, before his game was released, before the general public even knew he
existed... I suppose this all boils down to conflicting philosophies on how the game should be handled, but I don't think Greninja warranted his inclusion at the time that he was added.
That's not to say that I hate the character or want him to be cut; on the contrary, I'd love to see him become more prominent within the Pokemon series. But as of now, I feel that his inclusion in Smash isn't fully warranted.
Of course, that's just my opinion.