I think the main problems with class / job interactions is that it causes programming nightmares for developers.

Scholar and Summoner are a good example of this; because they both come from the same class, it's difficult for them to make adjustments on one job without having an effect on the other. And then there's more minor issues like having to constantly reset attributes.
And because Summoner comes from Arcanist, they cannot ever move it from being a DoT-spammer to a more 'traditional'-type of FF Summoner, nor can they do anything to Summon I / II because it would affect Scholar.


The same goes for a job like Bard. Because it comes from the Archer class, it can't have its own unique identity as a 'Bard'. And personally I think they squished these two jobs together just because they couldn't think of a way to balance a Ranger job that was full-on dd.

Existing classes also restrict future job options. For as long as Bard exists as an Archer class there cannot ever be a Ranger class in FFXIV, despite 'Ranger' being one of the iconic FF jobs (and not remotely related to Bard). The same goes for, say, Ninja; as long as Ninja comes from Rogue there cannot ever be a 'Thief' job in FFXIV.

There are potential opportunities for many things (job adjustments, future jobs, creating a unique identity) that would happen if the class system was done away with.