I don't think job simplicity really would hinder their ability to actually make replay-able content. In many circumstances they've already had the foundations for it in long abandoned pieces of content, some of them being related to the creativity of the content itself - One of the areas I'd really draw scope here that relates to myself is probably crafting. It's been a dumbed down system, and yet for all its flaws they did show that they could incorporate something fairly interesting, fundamentally (with experts), it just had some really weird execution in that all conditions were beneficial as opposed to detrimental. - I don't really consider that extent of a grind to have some replay value. - All I can really look towards in this direction with Deep Dungeons. It's a fairly simple system that just creeps with difficulty on each subsequent flaw. - Now I would argue this could be improved if they were to not really limit the floor count, but to essentially have the floors much less limited, perhaps 400, 500. They could borrow many mechanics from already pre-existing extreme or savage counters.
Now with this second point I really would be interested to hear your response in that.. What if lost actions and essences weren't necessarily just limited either to Bozja/Eureka. What if this were expanded and introduced with areas such as deep dungeon? They already have the foundations in the game for both of the systems, which in reality by your own admission already effectively addresses the job simplicities you took issue with. The simplicity is only as inhibiting as the creativity of the people creating systems, really. Personally, I wish content like deep dungeon or even Eureka/Bozja would be more akin to something like Dungeoneering from Runescape, where it'd effectively draw from multiple other areas of the game such as fishing for a key or crafting for an item.
The FATEs themselves haven't gotten better, really. But the incentivisation on them has improved significantly, courtesy of the gemstones system, which should also be expanded on. Grinds for better or worse are considered as content, it just depends how superfluous those grinds are as to whether it is detrimental. I don't think the game is quite there yet. They are necessary in some shape or form, especially for subscription based MMOs. For better or worse development time is always a limiting aspect, especially for content and creativity. So you more often than not need to lean on grinding-related activities to keep people enticed.