So, looking through alot of the threads involved with this subject I came up with an idea which I've smoothed out quite a bit more than I originally thought I would... The concept is both simplistic and careful of the game's structure and dynamic.
My thought is that the Armory system should belong to the job known as "Freelancer", which the player occupies until completion of the quest "Fade to White", after which the player unlocks a job sephiroth (much like the one seen in Final Fantasy tactics, but a little more... open from the beginning).
For those of you unfamiliar to the sephiroth (and not the villain of one of the worst FF games)...
http://www.brad.ac.uk/webofhiram/img/30sephiroth.jpg
For those of you unfamiliar with the Final Fantasy Tactics sephiroth of jobs...
http://squarehaven.com/games/PS-Port.../flowchart.png
The point? Using a very simplistic flow-chart of jobs to show how they all develop from the Squire/Chemist/Freelancer (a hallmark of FF3). The Freelancer job's trademark is the armory system- the ability to change it's play based on the weapon/tool held, and capable of combining several disciplines in fantastic ways. If the player becomes an exceptional disciple of both War and Magic, the player unlocks the hidden job: Onion Knight, which performs like a Freelancer- save that they get bonuses for both Disciplines of War and Magic. Other than Onion Knight,however, the game should not have jobs which must be unlocked by anything other than quest.
Other jobs however- are not reliant on their weapon choice to define their behavior...
The initial jobs:
-Monk: Disciplines of War and skills which are themed around a complex understanding of anatomy, physiology and spiritual energies
-Berserker: Disciplines of War and skills which are themed around making their user an absolute bulkwark or a devastating physical force
-Templar: Disciplines of War and skills which revolve around survival and indirectly punishing opposition
-Dragoon: Disciplines of War and skills such as elemental breaths, screams, jumps etc. the key elemental abuse melee job
-Thief: Disciplines of War and skills which revolve around the theme of "chaos". disorienting opponents, creating abnormal status conditions, lowering their accuracy and attack etc
-Hunter: Disciplines of War and traps and skills which buff the effects of battling with knives or bows, rewarding clever play
-Devout: Disciplines of Magic and powerful "over time" spells
-Magus: Disciplines of Magic and spells which require casting times, but hit instantly
-Summoner: The "pet" job. Disciplines of Magic and several ways of "blessing" the pet, and allied players
-Dark Knight: Disciplines of Magic and skills which revolve around increasing both physical and magical damage at the cost of HP/Defense etc
And that's a basic look at it, I think the Armory system is the perfect substitute of the "sub-job system", and should remain a major part of the game, and contribute to all players. But I also think it should be optional to master or only use Armory classes. I found that FF3's job system looks best if you remove the tiered jobs from it. I also think this concept leaves a great deal more room for expansion. Though, I would like the single limitation to be that job development happens separately from story development, so that there aren't "LvX" jobs, just simply that everything is available to begin undertaking after "Fade to White" with no limitations before undertaking a later story quest