I doubt they'd do another AoA adaptation. A re-do of the Brood Saga is what I would like to see. The TAS version was...weird. For Apocalypse they'd probably pull from the Twelve. Not a great story, but still a great way to re-introduce Polaris, Iceman, Sunfire, etc. Maybe even change the line up a bit and add Rictor as the fourth elemental and Rachel as the fourth Summers.
Since they brought up the Shi'Ar, I would love to see a proper Brood Saga adaptation!!!! They're already in their period-correct suites! I want to see Storm's galactic core feat ANIMATED!!!!!
I think the Twelve, properly edited, could be fun. It was such a misfire in the comics, it wouldn't take much to do a better version.
Let the flames destroy all but that which is pure and true!