I honestly think the game is already complicated enough - you have 3 heroes each with what 5-6 skills, then you get to juggle their items and your spellbook has 9 spells in it. On top of that then you have to think about 3 espers, each with 4-5 abilities each? O_o
There are so so many items (even the 4th level synth shop ones) that are not competitive with each other. I think it's safe to just remove the esper combat system (I did enjoy the boss battles, they were very epic). It's too hard to balance and it's had many bugs with trying to keep them in your spellbook, replacing your heroes causes bugs, etc.
Maybe just make it like...any time a hero levels up, they get +2 str if Faerga is under your control, +2 int if Anthanex is under your control, and +2 agi if the wind guy is on your team. Or just +1 if that's too much. This should be a passive thing and not like andenaj which you very awkwardly try to dance around on your heroes (I really hate that system too, I think andenaj is worth changing to make it not so awkward like swapping right before someone levels up =-=).