A well crafted post! There's some really great ideas listed there.

Personally, I'd be happier just leveling different classes. I like the ability to switch between different classes on a whim. Just because I specialize my Conjurer as a healer, I suddenly block myself from being able to play as a Black Mage? No thanks.

I think just tweaking the existing system to function more like the subjob system would grant a clear benefit to certain classes; adding not just abilities, but stat/trait boosts from other classes. Anyone could run a Whm/Drg, but to be a good healer, it made more sense to have a caster as a sub due to the stats. I don't have a many solutions on how to make it better/different from XI though, so I'll refrain from suggesting it properly.