I'm kind of iffy about prequels, for the same reason already mentioned in that we would be going backwards in the story. I would personally prefer sequels with expansions or a 3rd version with revamped storyline over prequels, but that's just me. It's not so much the AZ/Team Flare arc that's confusing, I think it's moreso about the Mega-Evolution plot. There's so many loose ends in both X/Y and ORAS in relation to Mega-Evolution that it ain't even funny. And then of course you got the Delta Episode adding the enigmatic Zinnia(whom, for a Hoenn-native, seems like she knows an awful lot about Kalos lore) and the possibility of alternate realities existing. There's also the whole Infinite Energy stuff talked about in ORAS, and NOW we have Blob-mon and Zygarde to throw into the mix. Lord knows I've forgotten they still have Volcanion to distribute before Gen 6 is done and over with.
What I would really like for them to do is this: make the new game(s) fix those Mega-Evolution/Infinite Energy connections between Hoenn and Kalos. I hope that this extra time that's passing between the release of ORAS and the inevitable new game(s) is a sign that they're working all of those loose plot threads out, but knowing Game Freak, I could be wrong.