you can make classes unique without messing with the current system of armory, and without having classes be really specific one trick ponies.
for example,
Warrior could have innate melee dmg increase, and a mechanic where every critical hit increases thier "rage" which stacks up and can be used by other warrior specific abilities, ones that can buff dmg, do high dmg weaponskills, etc
thf could have an abilitie that gives them a chance to strike multiple times with each attack, movement abilities like dodge and gain additional dmg to monsters that cant see them.
whm could gain buffs for curing up to a certain amount and sacrifice thier buffs to perform large heals, or special buffs as well as have a 30% healing bonus.
just adding these type of things on top of the armory system would make the classes unique, a whm would excel at curing above all others, but it would still give way to different playstyles, and there would be hybrid builds of value to different types of groups. The feeling of playing a warrior even with the same skills would be different than a thief, or a whm.
That said i think they should limit your weapon choices to 2 or 3 weapons per job, but not your skill selction. Your weapons of course will still effect your primary proffeciency, (like cure is a lot less effective without a wand) and your stats. (weapons have built in acc crit rate parry rate mattack etc)
i think that type of combination would make each job feel unique, but still allow a healthy playstyle selction. and of course certain jobs will excel at specific things more than others.