I've no idea where the ideas came from this time but...
1) Each spell can be used once per battle but cost no AP (exception: dragon skills cost a fixed 3)
With some form of scaling damage/healing power this should make more spells relevant than the newest 2-3 out of a potential 32 spell slots you have per character.
Implementation is easy since one unique enemy skill can seal spells until end of battle, so the same mechanic can just be used.
2) LP replaces AP; this is kind of a secondary HP bar.
If taken HP damage exceeds 50% of remaining HP you additionally take some LP damage relative to the HP damage.
Fatal HP damage deals more LP damage; if at least 1 LP remains the death is avoided and some HP is recovered (this replaces the chance to survive fatal damage via guts stat).
Overall this should lower the risk of getting randomly one shot just from AI roulette choosing the right/wrong action while putting a limit to how long you can get by with just taking 90% damage hits and spamming full heals while ignoring (de)buffs.
3) The condition stat (tired/fine/great, measured on a 0-255 scale) gets a bit more involvement.
By default it only seems to go up (neither many battles, day/night changes nor death did decrease it in my tests) and it is mainly responsible for a massive crit rate (both weapon and spells) at the end.
Resting would now increase condition to 160 if it was below.
Taking damage would decrease it by 1, more if LP damage is taken.
Having a bad condition would reduce the received healing, at most -30%.
Not sure if any other events should influence condition tbh.
4) The whole shaman fusions feel a bit underdeveloped; half of them come only near the end of the game and besides stats and maybe changing the character's unique skill not much happens.
So once you unlock fusions at all you can already use all 6 shamans for fusion but until you find the real shaman the relevant stat bonus is halved, e.g. without earth shaman you'd only get +10% defense if the real bonus was +20%.
Additionally you receive a small bonus to damage dealt with attacks of the same type as a fused shaman (fire shaman boosts fire weapons and spells, dark shaman would apply that to non-elemental) and resist attacks of the element (non-elemental only -25%, other shaman -50%) but take 25% more damage from the weakness (fire shaman gives weakness to water/ice).
5) Stat growth is half fixed by character and half determined by the equipped weapon type.
To that end most weapons would be equippable by all and instead of sword/bow/etc. we'd work with weapon enhancement crystals or something.
E.g. a wind type weapon would give higher AGL growth but less defense and earth type would give more HP but lower AGL.
6) Bleu gets actual stat gains instead of reading from the random encounter table.
7) Permanently stat boosting items get axed; will probably replace them with some tomes that can teach spells.
As written above, these are ideas. I've done some work on this already but not enough to be presentable in any way.
Feel free to comment on this madness.