Chances are, unless you're running an NSG game, and built up your aeons using all the excess spheres you've collected, you'll be strong enough to take out any aeon, even if they're maxed out. The most effective way to build up aeons is to level Yuna up, so most players will take that route instead of using spheres, which is a waste.
Personally, I prefer Anima in combat. Naturally strong, with a good natural skill set, and a great overdrive. She also has an edge over the Magus sisters, as you can't control them well in combat, and you can teach her abilities.
The Magus sisters, well there are three of them, and they can buff each other with magic skills, and they have a good overdrive. If you can get their morales up, to the point where you can pretty much control them, they can be a devastating force. Mindy has the unique attack called Passado, which fires 15 stingers at opponents, which can be really helpful during monster arena (and for you lucky FFX international players) the Dark Aeons.
I go with Anima, though. More easily accessible and more useful in combat. Not necessarily "the stroger", but hey.
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