Island Sanctuary:
It's fine as-is. Maybe the EXP can be sped up a bit now.

The Firmament/Diadem:
Outdated content but it's fine as it is. Modern innovations like Higher Stats and Revisit make farming a lot easier there.

Deep Dungeons:
Palace is fine but Heaven on High and Eureka Orthos need more of an incentive for players to run it that isn't "Clear it 4 times for a mount", since HoH isn't as popular and people level in Bozja instead of Orthos due to how braindead Z3 Mettle Farming is compared to the only deep dungeon where every telegraphed attack is a oneshot.

Eureka:
It already gives you Materia. It's in the Lockboxes that you get after killing NMs.
You'd know this if you actually played the content.

Bozja:
Bozja is good, the only problem with it is that other players don't know how to play to its advantages.
Infact, it would be better for the health of the zone's gameplay balance if EXP rewards were removed from Skirmishes and quadrupled in Critical Engagements, but reduced for each vuln stack that you suffer on each boss.

Delubrum Reginae:
They should make it so that if a party of 8 is queueing in, they don't need to wait 10 minutes for the pop. Barely anyone actually does 24man runs anymore.

Variants:
They're fine as-is, people just don't like it.
Maybe giving them a massive EXP payout would help, since that led to Aglaia being even more popular than Crystal Tower in Alliance Raid Roulette, even if it was only temporarily.