If N just said Genesect, that means little. According to the games, Team Plasma resurrected Genesect in general. We see little of Team Plasma. If he was referring to the Shiny Genesect, that's different. But regardless of that, they did refer to it in the movie as Awakening Forme(the Genesect/Mewtwo movie specifically) first. Anyway, could you quote exactly what N said, translated properly from Japanese and the Dub text? That'd help determine it. Saying Red Genesect would actually prove that particular one was canon, although many don't really fit. And as I said, I doubt the 3rd and 4th Mewtwo movies were canon. Mewtwo didn't technically refer to the original Mewtwo, she actually said that was her backstory, pretty much identical to the original's. It does actually matter if the second Mewtwo shows up in the anime proper due to the movies not being consistent entirely with the regular movie canon. Overall, they don't actually tie it into the anime in most movies, just a few of them. The one main thing is that Ash is always used, because he's Red's anime counterpart, so he's the logical choice. I think it's more of a cameo than anything, or just because Ash is severely recognizable that he's the perfect fit. He takes Chosen One to a whole new level.
Also, nobody knows if all the movies are canon, except the ones that directly are referenced in the Anime. Bulbapedia, a notable source who avoids stating facts if they aren't there makes it clear it's unknown. GameFreak nor the movie/anime creators have actually said they share a continuity, so it's up to the fans at this point.