I don't think it would be bad to make Limited Jobs/Advanced Jobs a thing. BLU BST PUP can have Limited Job stones and Advanced Job Stones. Limited is for the fun side content but not required AT ALL for Advanced. For Advanced, you learn the spells normally by leveling just as any other job. If you equip the Limited BLU stone, you'd have to learn them normally, but none of them would transfer over to the Advanced. It would just be side content/fluff/minigame stuff like we have with Carnivale.

For example, BST could be a ranged physical job like MCH and BRD, where the BST uses a whip and has a pet tiger auto attack not unlike the MCH's Turret. The Limited version of BST would be weakning mobs below 20% and using Capture/Tame on them to acquire an ability which summons that monster into battle to fight along side you. Then there'd be its own version of Masked Carnivale where you defeat waves of mobs using the most out of your pets to exploit weakness in mob type (e.g. Cloudkin>Vilekin, etc). PUP could be similar too, but instead of learning spells, or taming weakened mobs, you defeat mechanical mobs on the overworld/dungeons and collect parts/attachments or maybe have someone craft more advanced ones. Your pet menu could have 16-20 attachments which you build your Mammet up and change its logic (fight as a caster, fight as a ranged, fight as melee, give it oGCDs, etc). MIM/Freelancer could have the same thing but you mix/match GCDs and oGCDs from all the DoM/DoW you have leveled so far and complete content that requires various combinations of skills, e.g. removing Doom from yourself, beating a DPS check, tanking a big attack, AoEing something down, etc. The weapon or MIM/FRL could appear/vanish between GCDs like Noctis from FFXV. Like you do Chaos Thrust with a spectral spear, then follow up with a Souleater with a spectral claymore, etc.