MP represents your aetheric reserves, and at this point in the story it's clear that there's basically no job that doesn't rely on aether to function. In a perfect world, this would mean that every job would be designed to use MP as a core gauge in it's gameplay - each interacting with it in some manner thematic for that job.

In practice, it's easier to just design jobs from scratch with their own bespoke mechanics and resources, instead of trying to balance them around a single resource shared by everyone. This means MP has become vestigial over time, much like TP, with only the healers and small number of other jobs using it.

There's no doubt that it's a flavour fail, what we have is just a compromise needed to presumably streamline design development for the game. The answer is as simple as that.