Gordias Savage - Arm of The Father - Living Liquid. Thing broke my static within one month, and then we had to reform the group with new people about every month after that until we finally beat it 5.5 months after it came out. It made me never want to tackle another fight for that long ever again, so when Ultimates came out and people say, "Oh common learning time is like 4 months of 12 hour prog every week." I went with the hard pass.

Guildhest - Annoy the Void - and then any of the ones similar to it where you have to kill a boss. The guildhests are supposed to be teaching you to respect add phases and mechanics, but the mechanics are so loose in there, even before all these wild super potencies we have on weaponskills and spells these days, that you never ever had to respect them or learn at all. This sort of design choice echoed on into almost all other content where mechanics are often times kept so loose that people actively look for ways to ignore them so that the boss remains as training dummy as possible. God forbid you interact with it a little more than just hitting it as hard and fast as possible.

Any fight that they nerfed - Yeah, kind of a cop out answer, but a lot of great fights were made into pushovers like this and absolutely ruined because of it. Steps of Faith originally had enough HP with dangerous enough adds that it actually consistently would get to the 3rd Dragon Killer even with doing everything well coordinated. Having to shoot it in the chest with both of the bridge binding chains to keep it rooted so that a third party member could drop the dragonkiller on it without wiping the party was pretty dang cool. Add management mattered, and things really felt dire. I really liked that Vishap was so big and powerful that it could ignore you, as its only goal was to take down Ishgard's barriers. Being stepped on originally dealt like 4500~5000 damage, and was pretty much death for healer/DPS.
Siren in Pharos Sirius having to be Silenced or Stunned when it did Lunatic Voice to prevent the originally unremovable healing effect received down debuff while also flinging the charm on people where if they weren't full healed, they started attacking each other. To top it off, the adds spawned and more adds spawned, the crawling types could seize and immobilize your tank and healer completely. Quite a rough fight originally, especially if you had no BRD or PLD once she went stun immune.
Sunken Temple of Qarns laser telegraphs, final sting, and Qarn Facer spawns...