1. The battle for MT Hyjal.
Endless trash waves after every raid wipe rapidly get tiresome.
But the biggest pain in the arse was the mandatory requirement of a Protection Pally to handle the trash waves in TBC, this really screwed over Horde guilds who all had established warrior tanks for years and few pallies. Epic fail on design there Blizz.
2.Throne of the Four winds.
The raid with no story, the loot was only worthy of being nuked, and the RNG boss mechanics from Al'akir were beyond annoying (tornadoes spawning on your head, knockbacks into them/off the platform, and the fun of your character suddenly "appearing" in a tornado despite running yourself through the gap!) My guild hated it so much we skipped it after we got a single kill on him.
3. Firelands.
After hundreds of runs into Molten Core back in the day the last thing I ever wanted was to see Raggy again. The environment was too much like MC, the bosses were boring, and the gear looked awful.
He'd better stay dead from now on!