I think he is deserving, just surprising if anything. Greninja is one of the most iconic 6th generation pokemon because he is so interesting, most water starters were turtles, penguins, and otters, but this time we get a ninja frog. Don't tell me ninja frogs are not cool, because they are, ninja frogs are f**king awesome. Well, Ninjask is also a ninja, which is cool and all, but does he throw shurkans made out of water?
No he does not. Yes, Aegislash is also a very iconic gen 6 pokemon as well, but I think Greninja would fit better in a fighting game, since he's faster and seems to have more move options. Some people say Genesect and Zoroark should have had this spot, but they are gen 5 and I'd say Greninja is much more popular. With Mewtwo and Jiggs, there's nothing wrong with having 6 pokemon seeing that there were 6 pokemon in Brawl (Pika, Jiggs, Charizard, Ivysaur, Squirtle, Lucario). I think they could easily add both of them. However, in an unlikely case Greninja will replace Mewtwo, then no, I don't think he's deserving of the spot.