Given that the games didn't even go into much depth about the "dark" parts of AZ's story and mostly just dumped it on the player, I expect the anime could lighten it up in tone without changing the story much. Either way, they'd probably have to tweak it some to make it into an actual story and not the bunch of disconnected statements it was in the games.
If he does show up, they will simply glance over what he is and how he is involved. Probably just that he created this weapon and regrets doing so.
Step into the Fairy circle
They most likely cover the AZ with with a Team Flare two parter, with it ending with him reuniting with his Florette at end.
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Hope he not appears at all. I do not like him, find him a bit scary. Hope he stays out.
"Aint no think like me except me!" : Rocket Raccoon
Qoute from trailer and IMDB