I'd like to see a dungeon have some permutations that it might cycle through.
Like if you had a big bridge crossing there may be a low chance that a dragon just takes a giant Dark Souls dump on it and everyone has to go down below where a new path has opened up. Want to be careful putting certain rewards behind the permutations though since it might lead to people leaving if it's not the path they wanted, so this would be more for the gameplay mix up than the reward mix up.
May try optional routes but I feel the culture of the community makes that sort of a short joke outside of PF. I would however suggest using the dungeon assets for other content, like adding some DoH/DoL content, chocobo dungeon, perhaps new expedition content that lets you take squadrons into the area and build camps/outposts and you can extract resources from them after establishing certain zones. Like it might take quite a bit of effort but once you established a base camp at point 2 you could then go in as a crafter and use some unique facilities and resources. Like you might use the lava furnace rooms as a forge, or a specific area of water to quench materials (and with certain tiers of expedition progress you could turn them into valuable tools to use in homes and Cid's workshop if you don't own a homes, so you're not left out of content). This use of the resources but not within the 'DF' concept can also allow for some fun puzzles without having them be skipped or solved for you as well. In the combat might have some wild fun sometimes and go like Dynasty Warrior with you and your squadron taking out huge numbers of monsters lol (some expeditions could be methodically of course). Can find new secret mini dungeons when you excavate a humming rock, etc. If we had Wild Star housing this would have super massive potential, but alas we don't lol (like big project investments to make area's essence captures for your creation magic).
As for in general just want to keep seeing them trying something a bit different here and there. New types of scene movement, new mechanic/gimmick, the visual journey of dungeons is a big part of value to me so I like focus on that. Always little things to try to make it a bit different. Like the mentioned Dynasty Warrior concept, could have one dungeon feel like an open field siege onto a fortress, where you're this overpowered god sweeping through the fodder (at least until you get inside lol).
A larger aside though would be going back to older content, especially on certain jobs or certain levels, is often like 'eww...' lol. There are a number of potential solutions (with potential repercussions) but helpfully they are thinking about that. I like the idea that players who hyper sync down can choose to unlock parts of their kit (or their kit syncs potency down, which still is a buff but not as big) and part of the consequence of a dungeon that has some minor tweaks (few new adds or interruptible more painful spells) and aggression particularly towards them (not enmity modifications but monsters might go out of their way to slap abilities on you and such).