I would love to see jobs customization too! What if they left the classes but you can level them till you reach level 10, learning the basics, after that you choose a spec or a job specialization that will change your traits and main weapons with skill effects. For example:
Rogue Lv.10 -----> you choose between Ninja (katana), Thief (daggers), Sky pirate (sword + knife?)
Each job will have different stats(Thief on speed and crit, Ninja crit and medium speed and Sky pirate det and crit)
This is just an example, could be done in, if not all, most of the current classes and give them a sense to be there. BUT! I know could be a lot of work for the devs and wont happen