Yes. KotR has the highest mastery value, at 500,000 AP. Next is Magic Counter at 300,000, and there are a whole host at 250,000 AP; specifically, W-Magic, W-Summon, W-Item, Bahamut ZERO, Typoon, and Hades.

I have to agree with you regarding Underwater materia. It would have been awesome if that could have been exploited.