I found it incredibly easy to just cast poison on him when you enter battle and then throw your overdriven Aeons at him. Each time he banishes them he get's hit like 4,000HP or so, then the Morbis takes away some of his health to cure itself.

That pretty much screwed the Flux'er up, considering by Aeons did 9,999HP damage with the except of Bahamut doing 15,000HP damage. Also towards the end I just used Auron, Wakka and Tidus to do physical attacks doing 3,000HP damage and then poison.

Ah that was an easy battle yes? At first I was really stuck though, so don't worry.