Lets take these classes, Onion Knight and Onion Mage for simplicity, one being the base for DoW and the other DoM. As you level the class, you would learn "class" spells and skill. For instance the Mage would learn Cure, fire, protect, etc, while the Knight learns Provoke, second wind, invigorate. The weapons they can choose from would be pretty relaxed, melee weapons for DoW and staves/wands for DoM.

Around lv30, the class caps and the option to quest job souls becomes available, which start at level 1. These would obviously yield more job specific abilities such as flash/cover/sentinel for PLD. Once the soul is equip, obviously the selection of weapons is reduced to each job's main hand.This would allow for real diversity between jobs while still having a handful of low level abilities to choose from.