But what about the pentagons? What about Zygarde's secret moves? What about AZ's Floette? All the unresolved plot points like the ghost girl can be still addressed in future games, so they're not really relevant.

Zygarde's new forms and Ash Greninja can (and probably will) appear in the new games as well, but there was literally no point in putting those unreleased moves and forms in XY and ORAS if they weren't going to be available there.

Unless Gen 7 and Gen 6 are completely compatible with each other, like Gen 2 and Gen 1 were, meaning you can battle and trade between both freely.