While I don't see them re-vamping the dungeons they've already made, I think an 'extreme' version of dungeons for veteran players would allow new mechanics and to mix up what they've done before.

Why not mix up the bosses in different arenas. Maybe have some of the bosses walk around in the dungeon and be fought anywhere.
I don't see this happening due to the space needed for boss mechanics, but I would like to see the shape of boss arenas changed up a bit so it's not always a perfect circle. (like in Cutter's Cry)

Perhaps even have a random nemesis attack a party member who drops loot and experience points when defeated by the group, but disappears if targeted player is killed or party wipes. Maybe add an ally that randomly appears to help one of the players because of some high score they obtained in the at the Gold Saucer or they X amount of COMMs.
There's something similar in Sunken Temple with a Quarn facer that will drop loot, but run away if you don't kill it fast enough. I would like to see more of that as well, just to break up the momentum a bit. As for the random ally...It's hard to implement for story reasons, but I could see it as a fun diversion. You'd have to have a mirage/illusion-based dungeon for it to work, but it would be a fun mechanic where an ally comes to your aid, but the chance of it being a completely random character like Tataru or Lolorito or Brayflox or the wagon guy from the start of the game increases based on collective Comms. (Therefore being veteran players who have run plenty of dungeons and looking for variety.) I'd need someone more coding-minded to tell me if that would be possible, as I think Comms are saved Client-side and not on the game servers.

Why not add power ups from Deep Dungeon and Heaven on High to regular dungeons? Add more traps and elemental effect what weaken adds...
I don't think the pomanders should be added as that's part of what makes Deep Dungeon unique, but I would like to see more physical obstacles to out-wit or overcome.

Allow for visual changes to happen when a BLM uses thunder in water during a battle. Perhaps even allow the shocking water to deal extra damage to the adds.
You mean like in XV where if you use a strong enough Blizzard grenade (They're not spells, they're grenades and don't try to convince me otherwise.) on a lake you end up freezing your party in place? Yeah, that would be cool!

I just want to add we've been destroying so many machines in dungeons you're telling me we haven't once been able to pick up any Gatling/Rail guns to mow down waves of adds?
My first thought was of your profile pick just picking up a railgun and having at it. The second was "I could see Wedge doing that if you let him." Maybe tie that in to the ally bit above?