I like classes, simply because it makes the Job feel more special from a lore perspective. Lots of people are thaumaturges, anyone can train to be one! But you're a black mage because you're awesome. So it gets "discarded" in usage. I don't really think that's a bad thing.

The second reason is that I like one class being able to split into different roles like Summoner and Scholar. They should keep doing that, they just need to make bonus points a per-job thing when the split causes you to use a new primary stat.
The idea you're limiting jobs to X weapons or Y skills is artificial and fixable.