I only used aeons when required (Besaid fights, Belgmene, Isaaru), in the monster farm and on special occasions. Special occasions are like Anima in Macalania or Chocobo Eater on Mi'ihen Highroad.

Aeons are mighty, but they take away the AP, and that's not good. Till Zanarkand I actually try and get every character into every battle in order to get AP with all chars.

They're pretty nice in the NSGIENC challenge, though, as they also become stronger as you fight random battles. (Yuna's stats make that obsolete later, though)