It's definitely too easy to farm Economizers, so either the drop rate should be modified or the item should be removed altogether.

Most of the time, I forgot I could use the Esper as a summon instead of just learning magic spells from them. Something should be done to bring the Espers to the foreground.

In some cases, the character skills are horribly broken, mostly Sabin's Blitzes and Edgar's Tools. By contrast, I never used Celes' ability, nor did I bother with Cyan's SwdTech. That could be balanced better.

Those are the ones that jump out at me. It's been almost 10 years since I played FF6 so I'm sure I could find more if I played it more recently.