I'm currently using a blend of FATE Core and DFRPG to run two games-- a Spelljammer game and a game set between the "real world" and a grim and gritty envisioning of the Mario Bros universe.
Main change I've made to the magic system is that I've added more "elements"-- there are multiple characters with the Shadow element and one with the Wood element. I'm thinking about replacing the standard element system with something more akin to Legend of the Five Rings, with Earth, Fire, Metal, Water, and Wood and giving each of them "spiritual" qualities that replace the Spirit element. At least for the shroompunk game. DFRPG's standard magic system is actually a really good substitute for D&D magic.