I know the team is looking into changing the job class system....but here's just an idea.
You can only access skills from one other class you have leveled up. Your sub. It gives you abilities of that class of your current level.
Ex.
Level 25 MRD
Subbing a level 50 GLD
The MRD has access to all MRD 25 and below abilities and all level 25 and below GLD abilities.
Just don't do this limitation with job traits. Make it so you can cross class any and all job traits from all classes. SE just needs to make some unique traits to cross over.
This could make jobs more unique and find interesting combinations. Of course there will be cookie cutter setups...but that can't be avoided... SE just needs to make sure that each of the classes have very unique abilities and traits for this to work.
I made a bigger post about this in the battle mechanics forum...