Honestly, I personally don't feel Greninja was that out of left field, given that Sakurai always adds a Pokemon from the newest generation to Smash (Pichu and Lucario).
That said, I do agree that a deciding factor for Greninja, outside of his popularity, was how versatile and unique his moveset could be.
With Rosalina and Little Mac, it does seem that Sakurai is pushing for more uniqueness in Smash as a whole, given their unconventional gimmicks.
I don't quite think uniqueness is as much of a deciding factor as importance to a character's individual series, though. This is a bit of a stretch, but in Brawl, Sakurai did pick Wario over many other potential candidates from that series (including all of the wacky Wario Ware characters), likely because of his main character status. Still hoping for a Wario Ware character to be announced in Smash 4, though (perhaps Kat and Ana since we never saw their Assist Trophy in the Direct despite seeing the other Brawl ATs).
We also saw Lucas picked over the likes of Jeff or Duster (who both could have had very unique fighting styles).
So, yeah, uniqueness is important, but it doesn't quite trump importance to the series in my opinion. I think it is important to note, though, that ever since Ivysaur, the way a character fights is pretty much a non-issue.
Just my opinion, though. I could easily be wrong.