There is a lot of room for improvement in specific dungeons and specific encounters, but I thought I would first address several underlying issues that affect all dungeons and dungeon design in, I believe, an adverse manner.
1) Splitting dungeon runs into story and explorable was a mistake. Trying to find dungeon story groups is very difficult (lack of group finder does not help). Story modes are long, difficult, and completely unrewarding. You get one helm with terrible stats and and the same ugly texture shared across all dungeons the first time you do it, and really nothing at all the second and subsequent times. There is no motivation whatsover for someone who has done story mode to go back and do it a second time. Meanwhile, people who want to do exploration mode cannot because they have to do story mode first, but cannot find any story mode groups: they are limited to pairing up with other people at the exact same stage of progression they are – maybe 1% of the player base? People who have already done story mode and help their friends with story mode need to be rewarded appropriately.
2) Allowing people to graveyard rush down bosses is not very good – if players are failing at an encounter they need to know they are failing and they need to know why they are failing. The way people can keep rushing back from waypoints keeps them knowing they are doing it wrong. It replaces trying to study and learn the encounter with frenzied rushing back from the way point. It makes it seem like an intended mechanic – and they repair bills that pile up make them hate the dungeon. Additionally, the dungeons are absolutely rife with bugs and glitches, which makes players hate the dungeon even more. I go through entire story mode dungeons without seeing a single cinematic, because it’s bugged.
3) ALL DUNGEONS HATE MELEE PLAYERS. I haven’t yet seen an encounter where I would rather melee the boss than used ranged. I’ve lost track of how many encounters trying to melee will get you absolutely smashed and so you are reduced to using ranged. I understand that almost all classes have strong ranged options – however I am a guardian, which has the weakest ranged options in the game. I don’t particularly enjoy them. Speaking of ranged, it seems almost all bosses in a dungeon can be beaten by the same mechanic: every boss in CoF is pretty easy if you just keep running around the boss in circles firing with ranged weapons. This is not a particularly engaging mechanic. Likewise, all bosses in AC are easy if you just throw boulders at everything. Again, not particularly fun or interesting.
4) The number of runs necessary combined with the different paths means everyone will always run the most optimal path a million times. When you have to run the dungeon such an ungodly amount of times to get your armor set (more grind than in WOW, which is a feat) you don’t have time to waste doing the other paths. You will do the optimal path the 70 times or whatever it takes to get your set. This is a shame and wastes all the effort the developers and artists put into those parts of the dungeon. Plus you don’t get any tokens for helping out friends do their story mode. I don’t mind the tokens being dungeon specific: if you let the tokens be accrued in any dungeon, the playerbase would quickly just figure out the most optimal path in the most optimal dungeon and run that one forever.