Are you sure you're using the aeons properly, to their best effect?
First, before you go into the battle, make sure that all of your aeons are in overdrive mode - that they have the little orange bar all the way full up. That way when you summon them they can immediately do their most powerful attack. Also have Yuna at full overdrive, so that she can do a second summon on one of them (once they've done their own overdrive) and automatically kick them into overdrive again.
Aeons are never destroyed. They just go to 0 and become unsummoneable until the next time you hit a save sphere. So one of your best techniques is to fling aeon after aeon at a given monster to blast it with their uber-attack and also to absorb any really nasty attacks. Sort of a "shield" for your regular party.
So send your regular party to fight the boss, and then when you see in the little "order of combat" indicator in the top right that the boss is about to do something really nasty, have Yuna summon an aeon to do their one-massive-hit and then to take the damage the boss gives out. And if the damage kills the aeon, it's OK, the aeon has already served its purpose in that battle.