Blending Final Fantasy Tactics, Final Fantasy XI, Disgaea and The Elder Scrolls in a hypothetical on how The Elder Scrolls: Online classes could work.

To make this as brief as possible I'll represent this hypothetical more with visual aids rather than explanation, if you have questions, feel free to ask.

Character Level: 1
Race: Dark Elf
Race Bonus: -50% Fire Damage, +1 DEX, +5% Dual Wield Skill EXP
Main Class: Ninja (+2 DEX, +1 AGI, +5% Dual Wield Skill EXP)
Sub Class: Dragoon (+1 STR, +10 HP)
Custom Class: Shadow Dragon (if you want to name your combined class)

Base Stats and Bonuses (these are from FFXI and are just being used generically)

HP: 30 (+10)
MP: 16
STR: 7 (+1)
DEX: 6 (+1) (+2)
VIT: 7
AGI: 5 (+1)
INT: 5
MND: 7
CHR: 6

Abilities

Ninja ([X] means equipped/active, [ ] means not equipped/active)

[X] Stealth: Level 1 0/200 EXP (Enemies are less inclined to aggro you) (Passive)
[X] Dual Frenzy: Level 1 0/300 EXP (Increases the damage dealt from Dual Wielding) (Passive)
[ ] Resist Status Effects: Level 1 0/100 EXP (Lowers the duration of Charm, Frenzy, etc) (Passive)
[X] Subtle Blow: Level 2 150/300 EXP (Lowers enemy's damage of next attack) (Active)
[X] Dual Wield: Level 1 0/500 EXP (Lowers negative effects of Dual Wielding as other classes) (Passive)

Dragoon

[X] Call Wyvern: Level 1 0/200 EXP (Summons Pet) (Active)
[X] Ancient Circle: Level 1 0/300 EXP (Boosts Party DEF vs Dragons) (Active)
[ ] Jump: Level 1 0/100 EXP (Perform an extra damaging attack that lessens aggro) (Active)
[X] Heightened Damage: Level 2 150/300 EXP (Raises damage of physical attacks) (Passive)
[X] Spear Master: Level 1 0/500 EXP (Lowers negative effects of using a Spear as other classes) (Passive)

Weapon Skills

Left Hand: Sword

[X] Fast Blade: Level 1 0/100 EXP (Delivers a twofold attack)
[ ] Burning Blade: Level 1 0/100 EXP (1.5 fire elemental damage)
[ ] Red Lotus Blade: Level 1 0/100 EXP (2x fire DMG) (WAR / PLD / DRK Only)
[X] Flat Blade: Level 1 0/100 EXP (Stuns target)
[X] Shining Blade: Level 1 0/100 EXP (1.5 light elemental damage)
[ ] Seraph Blade: Level 1 0/100 EXP (2x light DMG) (WAR / PLD / DRK Only)

Right Hand: Sword

[X] Fast Blade: Level 1 0/100 EXP (Delivers a twofold attack)
[ ] Burning Blade: Level 1 0/100 EXP (1.5 fire elemental damage)
[ ] Red Lotus Blade: Level 1 0/100 EXP (2x fire DMG) (WAR / PLD / DRK Only)
[X] Flat Blade: Level 1 0/100 EXP (Stuns target)
[X] Shining Blade: Level 1 0/100 EXP (1.5 light elemental damage)
[ ] Seraph Blade: Level 1 0/100 EXP (2x light DMG) (WAR / PLD / DRK Only)

Then you have your other skills like crafting, lockpick, etc, etc.

To put this simply: Abilities/skills you equip are ones you learn, thus like in TES you learn the skills that you actually use. Basically it's actually molding the Perks into the actual Skills. Instead of just getting a flat +20% DMG from a Perk, you can now "equip" the damage modifier and level it up through use, if you wish.

Regarding the Main Job/Sub Job, it's done to create a tier system between classes so that some classes are specifically "better" than others at specific things. The Sub Job will have access to half of Abilities and Stat bonuses that the Job Provides. This way, if someone were to spec the following:

White Mage (Healer)/Black Mage (Destruction), they would heal better than someone speccing Warrior/White Mage. The WAR/WHM could still heal, but just not as well as the WHM/BLM, and thus they could focus more on their offensive role and provide back up heals if needed.

Discuss.