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Temple of Aminishi
In the second room with the Sanctum Guardian, the monsters outside the boss arena can still attack you even after you start the boss fight. It forces you to kill them or teleport out unless you want to get pelted with dozens of magic attacks during the boss fight. If you don't want to change this, at least get rid of that arhat that remains on the East after you leave and come back.
Masuta's big magic attack during his last phase hits way too early in the animation compared to his range attack in melee distance. If you're fighting the boss with melee, you have almost no time to react and have to resort to counting his attacks in order to predict when this attack is coming.
In the last room with Seiryu, there's pretty much no reason to kill 7/10 of the defence pylons since they're not aggressive and don't drop anything. Either make them aggressive again, give them drops, or add some other incentive for us to destroy them (eg. make killing all of them decrease Seiryu's defence or something)
Add some kind of indicator for when the "V" of hands is about to come out from Seiryu, as this would be a step in the right direction to make the boss fight slightly more melee-friendly.
For some reason the "V" of hands also causes a massive drop in frame rate for some people, and this wasn't a problem on release of the dungeon but seems to be the case now.
Dragonkin Laboratory
Both the Celestial Dragons and the Gemstone Dragons have massive defence towards melee attacks; way more than they do with ranged and magic attacks. It's especially bad with celestials because if destroy is on cooldown while they heal and your stun misses, there's nothing to stop them from healing. Slayer assignment for one of these monsters is almost required to make the defence more tolerable for melee. Either balance out the defense for all three combat styles or make it so that the celestial's heal stops even if the stun attack misses.
I don't think decreasing Astellarn's hp to 250k was a good band-aid fix to the fact that the boss' attacks are still having syncing problems (eg. sometimes the neutron star comes out before the wyrmhole is even placed). Considering how fast the boss gets shredded inside phase space, it just seems disproportionally short compared to the Sanctum Guardian and the Crassian Leviathan. If this issue gets resolved, please bring the hp back up a bit.
Right before you get to the checkpoint for Verak Lith, one of the lava strykewyrms on the path leading up to it can somehow snipe you from all the way down there. Not really a complaint, but just something weird that happens.
I don't really have to much of an issue with the "flying" phase during the Black Stone Dragon's fight, but what I do have a problem with is how sometimes when the dragon lands somewhere off-screen and tries to make her way towards you, the fire she tried to put down will instead appear out of nowhere very far from her. Sometimes the fire spawns right on top of you, and this has almost killed me on more than one occasion.
Similar to Seiryu's shadow hands, the spiral flame attack of the Black Stone Dragon causes a huge drop in frame rate currently, which wasn't the case on release.
Shadow Reef
There currently isn't anything special you can get from the Crassian Leviathan or Taraket, which seems a bit underwhelming considering how the first two bosses for the first two dungeons had uniques (fishy treats, Masuta's warspear, flurry & fury codices). Yes, the Ambassador drops t92 weapon components so there needs to be a balance, but just because these bosses can't drop anything too valuable doesn't mean they can't drop anything unique apart from their lore books (think fishy treats).
Some of the minibosses are so unnecessarily out of the way that it just feels like huge waste of time to go fight them (I'm looking at you, Cooper).
When the Ambassador does his sinister fragment shindig, add some kind of indicator for where the blasts are going to go. This becomes easy to deal once you learn where to stand, but is very unforgiving for people first starting out.
As long as the bug that causes monster damage to bypass all defensives upon death is a thing, there needs to be some sort of failsafe so people don't miss out on their drops from the Ambassador if they kill him during his magical onslaught. Either add some sort of way to prevent players from dying after the Ambassador dies, or add some kind of "claim-loot" mechanic to an NPC outside the dungeon just in case.
General Suggestions
As mentioned before with the Celestials and Gemstone dragons, all monsters in the dungeons should have equal affinities for all three combat styles. These dungeons should encourage players to use whichever combat style they're most comfortable with, and shouldn't penalize players who don't mainly use magic (which doesn't seem to have that many problems hitting in any of the three dungeons).
For the barriers that block off boss arenas when the fight starts, add a period of time where the barrier can be passed through from the outside-in (maybe like 5-10 seconds) before the barrier cannot be passed through at all. This way players can still get in the fight after getting blocked off if they're quick enough, but cannot just enter the battle later in the fight.
Add some kind of purchasable reward to the Elite Dungeon reward shop that automatically toggles off the reward chest's auto-loot only for the bosses, and re-enables it for regular monsters. Because this is more of a convenience thing, make this option super expensive (seriously, don't hold back. Make it cost over 1,000,000 tokens if you want to) so that it's more reserved for the really lazy people.
Make the Black Hands do a "got em" if the player dies, on a less serious request.