First of all, really cool! (Final Fantasy IX for the win!) Was just looking for a Final Fantasy IX magic stones system...The other stuff is really cool too!
I think for this project though, I'm only using that (combined with Neon Black's Passive Skills like you suggested), and perhaps the Synthesis one.
I, encountered a few problems.
One, was kinda strange, but it only happened with this script, I recreated the problem in the demo and it happened there too. If you make a skill that doesn't target an ally usable from the menu, it crashes when you use it.
Script 'SeM - Equipment Skills' line 1376: NoMethodError occured.
undefined method 'ap_window" for #<Scene_Map:0x9615f68>
Also, I wanted the bars back. "Gauges"? I tried to change the lines, and removed the # from the lines for HP and MP that I thought were for those, but once I did, when I try to go to the passive skills on a character, I get this: Script 'SeM - Equipment Skills' line 1358: FloatDomainError occured.
Nevermind, the problem was a passive skill that required 0 AP, and was thus automatically learned by each character, but not. Highlighting it crashed the project.
Also, for equipment skills...if a character knows a skill on their own, then equips equipment that can learn that skill, then they lose it when it's unequipped if they don't get the AP for it. This project has several ways to learn skills for characters (levels, skill shops, equipment skills, maybe more)...so, that's a bit of a problem.
Also, since not all skills are learned by equipment, and the 0 AP crashing I mentioned, well, I want some skills to not count as Equipment skills. No "learning" meter on the skills menu. I have no idea how to do that.
There's one other thing, it's a little more minor, special case, and might not be the Equipment skills problem. I want to have Passive Skills (using Neon Black's script) that give a character a new skill command type. It works fine, but the skill type doesn't appear in that characters skill list until I go off their skill menu and come back. I have a hunch it's the Passive Skills script. It's not major, but it's kind of awkward to have to go that extra step to see your new skills. It's the little things.
Sorry to mention so much, it's a great script!