I'd like to see a Merit system used to further differentiate Jobs from the same Class. Not much of an issue seeing as we only have Summoner and Scholar at the moment, but they're all meant to get second Jobs eventually. You'd just earn Merits on a Job, and use them to alter Class skills to boost that Job.
Scholar, for example, could change Virus to a buff which prevents one negative status effect taking hold. While Summoner could turn Physkic into another offensive spell. Bard could turn a few Archer skills into Songs or a way to recover MP to keep songs up longer (give Bloodletter "Restores MP" effect would be great), while Ranger (if it comes off Archer) could turn Swiftsong into a DPS skill.
It would somewhat fix the whole "If they add second Jobs, I have 50 whatever by default" issue. Yeah you'd already have 50 Ranger, but you'd still need to grind on Ranger to fully unlock everything.