Actually, they don't affect stats with use; they only affect stats if you happen to level up while the esper is equipped (a mechanic that I dislike, and one that, I found, is actually unnecessary, as the game is still on the easy side without it, to the point where I prefer to intentionally avoid those boosts while playing (or intentionally party wipe if I do accidentally get one, allowing me to keep the level but not the esper stat boost)).

If I were to make a simple hack of FF6, I would do the following:
* Eliminate esper stat boosts
* Make Ultima not ignore magic defense (the spell is so powerful it ruins late-game balance as is, and this tweak still makes it better than flare/meteor most of the time)
* If hacking the GBA version, allow Gau and Gogo to equip the Merit Award again (I especially dislike how they made Gogo unable to equip it) (For anyone who's thinking about the PSX version, that version is probably not worth hacking, and there's a glitch that makes the Merit Award unnecessary for giving Gau weapons.)

Of course, this is assuming I ever feel a desire to replay this particular game, which may never happen.