Well considering Jobs only just come out, and they only just rebuilt the classes a few patches ago it's expected there is going to be some tweaking involved to make the classes / jobs distinctly stand out from one another and be balanced.

Even without class stacking a majority of the content isn't so difficult it can't be done, they just have to make content that doesn't encourage stacking like it does with speed runs.

But if you want to really make classes distinct, I'd say kill cross class abilities on the Jobs and add another five abilities to define that job even more. There's no reliance on abilities from other jobs, nothing to help make them OP or versatile, it's all you and what you can do with what you got.