Thanks for the suggestion. While not a bad idea, the change would require some reworking on the equipment, which I can do, although I am unsure whether I want to do such. Seeing as AP Skills also come from weapons, having a limit of 1 AP skill isn't really a limit of 1, as you'd still sometimes have 2, and the ultimate work around of either not having AP Skills on weapons or only having AP Skills on weapons doesn't sound fun to me. That said, I really appreciate the suggestion, and will look into ways to address it in the future.
I don't know what plugins exist for MV, but my ideal solution would be for the AP skill to be its own system entirely, instead of being done through equipment. If multiple AP skills were "unlocked", this system would let the player pick one externally from equipment slots. I wouldn't know where to begin on doing that, though, and it's quite playable as is
I look forward to future development on the game!