Maybe one way of solving the "everybody ends up alike" issue is that instead of everybody learning the same spells from the Espers, have them learn certain "special" abilities from each one. Using Sabin as an example, this could be anything from a Blitz like "Chakra" from Starlet, or a stat boost from Cait Sith. Others, like Edgar & Mog might learn a jump ability from Palidor. Only a few characters would learn magic, such as Terra & Celes.

Albeit, the only setback might be that relics like dragoon boots would become more useless than they are now.