After playing through recently, I've come to realize how easy the game can be. When I was in elementary school, I thought it was much more difficult. Now, I just semi-low leveled (only fought enough to keep properly equipped) a game so I could min-max stats with the best espers, and it was surprisingly easy even before I started to grind out some levels (except for one battle with a brachiosaur and a mistaken save state).

Warning: I start getting creative/messing with the game itself.

My suggestions (most of mine have already been suggested, and I'm likely repeating ones I really like):

Esper System Tweaks:
- Characters must learn Summons similar to spells, but can only cast them when equipped with the respective magicite.
- Make summons better (important for my other ideas on summoning; if its more restricted, it should be more difficult).
- Better distribution of stat bonuses; bonuses for other stats.
- Limit ability of characters to learn spells; when every character but Umaro can cast Quick and Ultima, its not too intense. Not positive on how to do this.

Stats:
- Make Stamina useful. I say make its main purpose determining HP, rather than usefulness of regen/poison. This would also make stamina-boosting espers better.
- Possibly more stats? Luck, agility, etc.
- Characters could have innate elements, strengthening their attacks with the proper element, weakening it with opposing. Always felt weird to see Terra casting Blizzaga/Celes casting Firaga.

Characters:
- Make more of Sabin's Blitzes physical. Its silly, plot-wise, that it makes more sense to focus on his magic power than strength. This is a man that can hold up a building, can suplex a train. Why should it make any sense that he should be built as a mage, while his brainy brother would get buffed up?
- Only Terra can Summon/only when morphed. If only when morphed, she should be able to repeatedly summon in same battle (or perhaps can summon once/battle normally, unlimited while morphed). Similar idea, have Morph be similar to doublecast.
- Strago and Relm should learn proper magic similar to Terra/Celes.

Gameplay/Plot (this could get me in trouble):
- Non-torroidal map. I don't know if its too much to have an actually properly globe shaped map, but that bugs me in every FF game.
- More opportunities to use Magitek armor. Cuz thats just fun.
- More scenarios for the full party to be split. Most obvious opportunities:
While searching for Terra, remaining party continues to defend Narshe from further Imperial attacks/entirely new quest.
While travelling to Opera/Vector, same thing.
While travelling to Thamasa, remaining party spies on Imperial activity (more involved than just 'Edgar seduces the maid').
In World of Ruin, give every character their own scenario; make Celes's the last one you can complete. So, they all get their moment to shine in the intervening year before Celes, Edgar, and Setzer (and Sabin) start re-uniting the team.
- Make Floating Continent a multi-party dungeon. Cuz those are just fun.

Equipment:
- First, more limits on who can equip what. Force more characters into division between light/medium/heavy armors. Also, no shields for relm/strago/sabin/etc. Or, only light shields (but more light shields, and qualify less of the shields as light). Also, more division on swords; I don't want Locke with the Ultima Weapon
- No more relics. Well, not exactly. Make relics both rarer and types of equipment. In other words, more equipment slots (helm, armor, greaves, boots, gauntlets, rings, necklace), and have occasional equipment that grants the bonuses that relics do. Kinda like how most western-RPGs are (Dragon Age comes to mind).

Those are my modest proposals. My less-modest proposal is that someone makes a Final Fantasy 6 total conversion mod for Dragon Age/Skyrim/Whatever.