This is what I was thinking too, sorta like how you chase Suicune around in Crystal/HGSS. It would be cool if the story had you chase the Dog-forme around the region and help it collect cells so that it can power up and become the Cell-forme, and then finally culminate in Perfect-forme at the climax of the game when you fight the bad guys.
As for Greninja, my first impressions were that it was its Mega, and that it's design / colour scheme was influenced by what its trainer looked like, so the way you customised your character in-game would change it's appearance. However now I believe it will just be an anime thing, maybe a special event like CosplayChu. From what I can tell, Greninja is quite a popular mon so it wouldn't surprise me if it got some special treatment. I do think we need some gen VI Megas though, and what better time to introduce them to us than in the second time through Kalos? And with the starters no less...
I've seen some complaints on Facebook regarding the 'trend' that GF are taking with the third legendary in each trio from gen IV onwards.. Apparently some people are sick of the pattern where we get an 'incomplete' legendary in the first round of games (Giratina, Kyurem and Zygarde), and then have it receive an upgrade in the follow up games (Giratina-O, Kyurem B+W, and now all these Zygarde formes). Personally I have no idea how this is a problem, if we got the full version of the third legend in the first games then what the hell are we meant to explore in the follow ups? lol. I suppose I'm wondering what you guys think about that (since it seemed a popular opinion where I was reading).