I guess I would be approaching it with the idea that players should choose their difficulty. Let's say you completed the new dungeon. You unlock "shifting" version of it. In there you get options such as:
"Bosses are more complex"
"Bosses have a time limit to defeat them"
"Mob pulls are more complex"
"There is a constant DoT effect happening"
"Tanks take more damage"
"Occasional clouds that seal weaponskills and spells appear"
"Everything has more HP"
and so on. Nothing too hard on it's own but when all is chosen it can be as hard as Criterion Savage. Players can choose the difficulty they want to have while playing with friends or PF. Or randomly put into an easy preset (such as "DoT + Clouds") when using DF. For rewards it can give coins that can be traded for Augmentation materials, Materia, or even gear. Same can also be applied to extremes and savages should raiders want to challenge themselves or train for Ultimates or whatever.

Secondly I would change how the syncing system works, such that your stats and your abilities can be synced independently while you're in a group. Want to do an old dungeon with level 100 skills but that dungeon's item level? Now you can. This change will help Unreal content I think. They can just put content from older expansions randomly each week to rotate.

For the content design itself I would include moments like Mountain Fire from the DT EX1, even in normal modes. A tank buster that creates a safe zone around the tank. A tower that splits the arena so that ranged players can still attack while dealing with stuff there. And so on. It should feel good that you are the one whose interacting with that mechanic because of your job choice. Players should feel "I'm glad I was the [Insert Role Here]." when doing those. There are some mechanics in DT that feels like that (look at Mountain Fire from DT EX1) and I think there should be more of that.

For job design.... I don't know there is a balance to be struck between making each job unique and making sure each job can clear every content. PvP designs oozes with personality, so they can take some clues from there.