I've been kicking these ideas around in my head for a bit and I've noticed similar thoughts crop up in various social media and conversation I've had with other players. So I thought now might be a good time to put them in print. I don't really have a structure for this so I'm just gonna list my thoughts.
Optional Routs: This can be diversified in multiple ways and can be as simple as choosing between door A or B. Obviously the meta-game will pick apart this system so there will always be a "best rout". But at least having an option would provide some welcome variance to instances many of us grind daily. A good example of this in game is Thousand Maws of Toto Rak.
Skill based Options: Provide optional content unlocked by players who posses the correct skill. For example, poison gas blocks a hallway to an optional boss. Any player possessing 1 level or higher in Alchemist can quickly access plants or maybe a work station in the area that activates a buff for the party which negates the gas so they can enter and fight the boss. Another example could be a breakable wall that any party member possessing a level in Miner can activate to open a hidden optional rout.
Environmental Hazards: Rock slides, cliffs, pit traps, pools of acid/lava/etc.. make them deadly and make them interactive. I'll use the rock slide as my example. The party can target and damage the trigger to set off the trap to avoid it or lure mobs into the hazard zone and use the rock slide to their advantage. This should hopefully inspire tactical thinking and reward clever players.
Parkour: Climbing stuff might not be that interesting in and of itself but adding verticality in combination with other elements would bring dungeons to a whole new level within FFXIV (pardon the pun). Imagine having to fight a boss on two floors where a transition phase floods the lower level with water and drowns anyone unable to escape. Or perhaps players need to climb to a second story to trigger special environmental hazards that can inflict massive damage. Parkour could be something that is rewarded on its own like having jumping puzzles to hidden loot or optional routs and bosses.
Alternative Modes of Navigation: Keeping things confined to just the player inside an environment there are still a lot of ways to get from point A to B. Stormblood will add swimming and I would love to see this implemented into dungeons in some way. Other localized modes of travel could include swinging over a chasm on ropes or vines. A great example in game is the Weeping City were the player dives into rapids that throw them over a waterfall.
Hidden/Super Bosses: A special optional challenge at high difficulty that could reward something other than dungeon loot. Maybe cosmetic items, achievements, bonus tomes, or titles.
Okay, I think that's it for now. Hopefully it wasn't too hard to read.. I tried not to ramble. So, thank you for reading if you've got this far and maybe add ideas of your own.