materia as suggested in the OP would make the game for fun and dynamic for sure, and would probably be a major draw simply by virtue of encouraging more players to experience more content to get the materia they want- but it would probably be a nightmare for the devs to balance it all correctly, and certain classes and materia combinations would be completely overpowered and broken for stretches of time while they figured out what to do with it.

maybe that's something they can actually afford to do in 2.0 when the entire dev team is working on the same game... but for now it would just be too much work, i'm sure