I like a Final Fantasy Tactics approach to obtaining advanced jobs. However, instead of "training" in certain classes and obtaining X number of abilities, you would first set a number of abilities, which would open up the option to choose abilities from the advanced jobs.

For example, by setting 3 GLA abilities and 3 CON abilities, we open up the option to select abilities from "Paladin" job; by setting 2 GLA abilities, 2 CON abilities, and 2 THM abilities, we open up the option to select "Red Mage" abilities and traits. This way, not only are advanced jobs "advanced" due to the fact that it requires a certain number of action points to set the abilities needed, but also preserve the current armory system.

Also, it allows players to further customize their "advanced jobs". If I chose to be a GLA primary, my "Red Mage" would be a melee caster, or if I chose THM as main, my "Red Mage" would be enfeebling focused. And because abilities aren't limited by class, I can choose to be a "Red Mage" as an ARC, PUG, or LNC, not just restricted to the 3 classes that the abilities are taken from. The only weakness here is that some abilities wouldn't be as optimal due to affinities, but the option of playing a Red Mage that uses bows as primary weapon is still out there!