Hmm, what is the difference between Zygarde's Formes and Ash-Greninja? That's a good question, and honestly one I can't think of a direct answer for. The only answer I can think of are sketchy but to me they sound good enough to distance the two:
Presentation: Let's look at how they were shown to us in the anime. Zygarde Formes were rather randomly introduced; in the anime we saw Team Flare experimenting on a Zygarde Core (and a few Cells) and also going after a second Zygarde. It felt like the writers were shown Zygarde was getting new Formes so they wrote them in as soon as they could, as if they wanted to get them in before a game came out with them in it. Ash-Greninja meanwhile was built up. We were told Ash's Greninja will save the Kalos region (which BTW was also a bust, did it do anything specifically to alter how things went?), when it evolved it then revealed it had a strange transformation power but we couldn't see it clearly, then after some development Ash and Greninja finally mastered the transformation. This more felt like the writers had an idea and slowly developed the idea, foreshadowing it so the viewer wouldn't be completely caught off guard with why Greninja can now go super saiyan. Also it replaced Ash's need for a Mega Pokemon which I see as another red flag.
Tl;dr, I feel Zygarde is a bit more legit as it felt was shoved into the plot so it was in there before the games while they took their time to develop Ash-Greninja seemingly now worried when the next games were going to be announced (since it wasn't going to be in the games).
Design: This one is simple, Ash-Greninja looks like Ash because its formed between Greninja and Ash. So unless you're Ash, you can't turn your Greninja into Ash-Greninja. The closest thing they could have done was what
Codraroll described (and I had described many times previously): in Z the Starters final evos would have a super form who's appearance will be dependent on their trainer's model. However we would never know, but the point still stands with Ash-Greninja. The Zygarde Formes are their own thing, there's really nothing stopping anyone from saying "well Zygarde can't be put into the games because of (reason here)".