Your starting espers go by what your types of characters are. Melee characters get melee espers, flying get flying, healing get healing, etc. I believe a character will get the highest level esper that matches their type. For example, if you have a level 2 melee and a level 1 melee esper selected, I think your melee character will get the level 2 one. If you have two melee characters, I think they'll get each get one of the level 2s and one of the level 1s.

As for level 3s, I don't think you CAN use those unless there is a summoning gate.