Except that's what Sakurai said, he stated that his team were given the designs of the Gen 6 Pokémon, saw Greninja, and went with him. Nothing that has been said or done by either Sakurai or GF since has shown that the latter was whispering in his ears saying "pick Greninja!" They haven't advertised it anymore then Delphox or Chesnaught, it didn't get a bigger role in the movie then the other two (in fact, I think Chesnaught's was slightly more notable in it IIRC), no toyline differences, manga appearances, etc. If they really had Sakurai put him in with the intent of marketing him, they haven't been that successful in that regard at all. It's just been treated as another starter so far.
As for why they didn't pick Chesnaught, we don't know. Nothing says that he couldn't have picked him (or Delphox) considering he's a starter and comes with marketability based on that, it just wasn't in the cards for him at that particular moment.