Arrange has some balance issues end-game at the moment due to the .exe modifications to materia bonuses/penalties.
It's been a while since I last played, and I just installed everything and noticed that. Amusingly this was enough for me to mess around with WallMarket to try and fix some of the unyet-fixed issues I spotted (mostly things with the armors), but most of it was forgivable.
I think the biggest issue is how the stat reductions are used at the moment heavily encourage physical damage builds over magic builds, which isn't an issue early-game, but a serious problem late-game given how steeply a lot of the materia reduce physical and magical defense. The magic-materia have no issues with how they are set up, it's the support materia where this is most problematic from what I can see.
Magic casters NEED support materia in order to be useful as casters, and some of the best support materia are too negatively stat-reduction heavy at this point in time to be of use for those types of magic builds.
Thus it means that you should be considering alternative stat bonuses and reduction setups to deal with that. It's one thing if the reductions also give some useful bonuses, but that isn't really the situation with the support materia at this time (the command materias are also almost in the same boat, with all of them being too similar to eachother from what I can see).
That said, what you did with the "HP <> MP" materia is quite honestly genius, and works nicely for both Cait Sith and Vincent given their abilities. Amusingly were there a Relic that could allow characters to lose MP in place of HP when they take enemy damage, it would make it worth using that materia and relic, and would make Vincent and Cait Sith have some fun uses given what could be done with it.
Anyways, I'm starting up a new play-through, and I'll give commentary and screenshots as I go through things and if I spot any issues.
EDIT; Ok, first issue found. Right after the Reactor 5 mission, when you get Aeris/Aerith as a party member, the innate ability description for her contradicts itself. Here's a screenshot showing what it covers;
And here's a screenshot showing what it does not.
Second Edit; Pretty suspicious indeed (broken text box).