Right now, most Classes are basically just "low-level Jobs". However, I think there is room to make the Core Classes into proper Jobs.

WHY:

Thematically, core classes are very different from their later Jobs. Despite sharing skills, Paladins are nothing like Gladiators; one prides itself on protecting people, while the other fights for fame and fortune. Marauders are supposed to be pirates, while Warriors are primal, tribal warriors harnessing their inner beast. Many of the Disciples of Magic could return to their 1.0 incarnations, with Conjurers using more nature-oriented spells, while the White Mage would use more "holy" spells. Core Classes are generally a little more "grounded", but still fill some really cool fantasies.

The real benefit, however, is that is changes a Class's given role. Gladiator and Marauder would become DPS, Conjurer might become support-damage, Lancer becoming a Tank, etc.

HOW:

At level 35+, you get one additional quest to "Master" your Class, providing it with its own Job Crystal. Equipping it might remove or replace certain abilities.

The idea is to completely change the class role, or at the very least, modify it. Gladiator would lose its ability to equip a shield, but instead dual-wield (like our man Raubahn... used to). Shield abilities would be replaced entirely, as well as losing Flash. Marauder would retain use of its two-hand axe, but it's abilities would change to have DPS-oriented functions and new visuals (ie. Overpower is replaced with pure damage, and a sea-spray instead of flames), and overall more nautical abilities (maybe throwing out an anchor instead of Tomahawk?).

In the case of a Lancer, I would personally make them into tanks, being grounded fighters. I might even suggest letting them equip a shield, wielding their lance with one hand to jab at enemies, almost like Spartans. Archers would remain DPS, but perhaps made more focused on pure damage, whereas Thaumaturge might become more support-oriented damage (ie. AoE that both heals and damages those within range).

SUMMARY:

Classes would essentially become "Alternate Jobs", using similar abilities to fill different roles in groups. As well, they would cater to different player fantasies, as opposed to ONLY the classic Final Fantasy jobs.