Well yes, though I'm not sure if overhaul is the best word.
To elaborate a bit more, I fell into a few rpgmaker traps, after coming to the realization I thought it would be best if I went back and fixed some of them before going on.
Characters werent different enough from one another so I'm now limiting all characters to three unique commands and changing a few of what current commands do. Example: Thanatos' "Alchemy" command was just a dressed up magic command, now he'll have the standard Arcana command, and an alchemy command; which will behave a lot like the Geomancy skill from FFT). So instead of having
Fang - A regular attack that just drained mp
Alchemy - Different named generic magic command
Alchemy - An MP free magic attack that varies depending on the enviroment.
Arcana - Standard Magic Command
Item - Item command (As an Alchemist, Thanatos can use certain items other characters cannot)
The introduction did a poor job of foreshadowing so it's being completely redone (actually this part is pretty much done).
The activities that follow after you first get control of the real protagonist I'm also not very happy with, so that's getting a bit of touching up.