Started as a wild tangent off someone else's idea but I thought a sphere grid / license board / merit system that was purely glamour could be quite good. Since we just toss exp off the edge into the Atomos abyss right now.

As you say in the OP it could be used for changing the appearance of skills, giving players some different looks. SMN could have upgraded egi visuals for example, maybe for "immersion" you have to go dump the exp into the shrine of that primal like a pilgrimage lol. Dark Knight getting his smokey shadow effect for Dark Side.

Job specific mounts and minions that you can unlock. Some can be goofy like Dragoon unlocks dragoon jump mount (which basically gives you moon jump in flying zones). New glamour gear, especially thinking of things that normally break glamour restrictions, like white mage might be able to unlock holy breast plate (heavy armor chest plate). If not a special job (some sort of war geomancer new top of job) I think Golbez / Ex-Death armor would be pretty neat for the mages.

As pointed out though they'd first need to build a system to replace animations and also share that info with others, like equipment almost, and that might be a lot of data/stress on the server. The other concepts in the sphere grid could still work (like mounts or armor) but I feel animation replacement would be the most challenging part.

Would be neat if possible though, further customize our characters.