I think a 2:1 class:job system could be very interesting. Let each class have its own job and a job it shares with another class.

Example:

Conjurer - White Mage (req. CON30 + THM15)
> Red Mage (req. CON30 + THM30)
Thaumaturge - Black Mage (req. THM30 + CON15)

Once you've met the requirements for Red Mage (CON30 and THM30), and completed the proper quest, you can equip the Red Mage Job Stone on either Conjurer or Thaumaturge. By doing this, you can choose to be a Red Mage which uses a wand and leans more towards Healing/Buffing Magic, or one which uses a Staff and leans more towards Nuking/Debuffing Magic.

Now, there might be a better choice than Red Mage for this example, since it doesn't provide Red Mage with a Sword or other melee weapon, but this is just to illustrate my vision.

Another example could be

Gladiator - Paladin
> Berserker
Marauder - Warrior

A Gladiator Berserker would use a Sword and Shield and have more defensive capabilties, whereas a Marauder Berserker would use a Great Axe and focus on an all-out offensive.

Again, these are just examples to illustrate a point. I didn't put a whole lot of thought into the actual classes suited for each combo.

And who's to say each class couldn't branch off even further? Each could have one "Basic" job and two "Advanced" jobs.

Rogue - Ninja
>Thief
Gladiator - Paladin
>Berserker
Marauder - Warrior
>Dark Knight
Lancer - Dragoon
>Samurai
Pugilist - Monk
>Dancer
Archer - Bard
>Ranger
Musketeer - Cannoneer
>Gun Mage
Thaumaturge - Black Mage
>Red Mage
Conjurer - White Mage
>Summoner
Tamer - Beastmaster
>Geomancer
Arcanist - Time Mage
>Blue Mage
Rogue - Ninja

And they wouldn't all have to be linked like that. There could be several smaller rings of connected jobs. Obviously that's a lot of jobs and classes to balance, and it would take a long time for it to get that fleshed out, but I think it could be really cool.