I really don't understand why some people are upset, not to mention a handful of people don't even explain why, They just say they hate it.
I for one love Ash-Greninja in the games. And this could indicate that Chesnaught and Delphox could get something similar later on. They did the same exact thing with Blaziken. People were upset because Blaziken got a mega and the others didn't, however, they already had plans for the other 2 starters. Just like they may have plans for the other two Kalos starters.
I don't think it makes Ash canon in the games. Hell, they basically made Alain canon in ORAS, so why can't they make Ash canon? Red and Ash are not the same people. They can easily coincide with each other. They don't look like each other at all. I just don't see a problem with it.
And even though they will need an explanation, it shouldn't hurt.
They said it all comes together. I think this is what the partially meant. This isn't the first time they have crossed anime stuff over into the games.