I want to correct this, Final Fantasy 6 was actually terrible for item balancing. The game is my favourite, but the entire game is entirely broken lol. Items were very strong when your only sources of healing was Terra and Celes, so the early game. Once you're able to actually use Magic, Items like Ethers and Potions are basically useless because you can just Cure to heal, and Osmose to get MP back, and 99% of the enemies in the game you were able to drain MP from. Sure you'll use them between battles to set up for boss fights if you aren't near a save point for tents, and even then you could just Osmose during battles cause unless you were critically underleveled Final Fantasy 6 had no challenging fights. The game was incredibly broken once you learned how to use magic, and was broke even more if you used Esper Stats properly.
THAT being said, Items are still important. Look at Legend of Dragoon, Items were super important in combat. It was your main source of healing, how you did elemental damage when not in Dragoon phase, and where majority of your buffs came from. Healing Potions found early game, were still important at the end of the game because they're percentage based so you never risked only healing for 200HP late game with a Potion like you do in Final Fantasy.
It comes down Items or Magic, one or the other will be better but they don't have to invalidate themselves. You could have items be stronger in the early game, slowly get passed by Magic and then have a new set of item (like Hi Potions) become frequent and pass Magic again until Magic scales up again. If you're having Items and Magic fill the same role, you could have Character Abilities be stronger versions of the Items, ie. Fireball VS Fireflask, one does 200 damage one does 150. But have the items somewhat common, while MP Restoration is rare at the start so it comes down to if you wanna use the item, and save the MP or use the MP to end the fight faster. Or you can follow the Legend of Dragoon route, have most items be single target spells, while Character abilities are AoE or offer something else on top of it, but MP management is rough early and the game isnt balanced around it. Honestly with what you've said, I'd look into Legend of Dragoon and see what you think of how they handle items.