I know that Zygarde was hyped up a lot with its forms and the anime title did make me think we'd get something like XZ/YZ, but the fact that they only showed them in the anime artwork should have been a tip-off that they weren't planning on featuring them in a main series game all that soon. That's not to say that I think they'll stay anime exclusive. There's already other merchandise for them like the cards and I think they were featured in Pokemon Picross, but I don't think that they had planned out anything major for Zygarde, despite the hacking revealing those two moves. We can still have Zygarde featured in a post storyline to make fans happy and I wouldn't be against it, but I'm kind of glad that it isn't the main feature of its own game. I feel like fans put it on a pedestal primarily due to the patterns more than anything else. Even if they did release a Z version, I would have bought it and it still could have been enjoyable, as I do like most of the third version games, but Sun/Moon were much more unexpected and have more promise as a new generation.
As far as Eternal Floette goes, I don't think that is much of an issue. Like with the two moves, we only know about that through people hacking into the game. While I seriously doubt that they ever had plans for Z game to scrap, I could buy that they original was going to have an event with Eternal Floette and dropped it for whatever reason. There is still plenty of time to do something with that through an event before Sun/Moon comes out, but I don't see much of a need for that. At least with Zygarde, I could see it being featured in something like a post storyline, but not so much with Eternal Floette. It's tied into AZ and his story was pretty much done at the end of X/Y. It wasn't handled nearly as well as it could have been, but it was wrapped up.