One question. Is there a way to change whether skills are effected by these things, the support UPs, shell, protect and zodiac compatibility?
support ups/shell -- yes. that's a simple fftpatcher function
zodiac... not so much. You can change the formula to be a zodiac-immune one and work that angle, though.
Edit: Defensive support ups, yes. Offensive... not without some hacking.
You mean the little squares in the AI section of a skill for the Defensive UPs?
upper most section? Yup.
For example, the cure family by default negates MDU/Shell, while fire family does not.