If we're going to talk about clusterfucks, I think Odyn, Helya, and Botanist are the biggest offenders - there's just too many movement-based mechanics going on all at once, and if you're playing a caster you rarely get a chance to actually turret.
But the rest of the fights are fine IMO, and I would definitely like more fights like Ilgynoth, Cenarius, Spellblade, and Elisande in the future.
The boss rooms in NH are either too small, like Skorpyron with a million rainbow colours in a dark environment or Tichondrius with it's retarded camera angles due to the ceiling and walls being too close, too big for non-mobile classes, like Anomaly and Gul'dan.
Every other boss room is sort of all right, given the mechanics.
The trash however, it's not. Either way too much of it or with irritating abilities.
Not directly related but I must say I find Nighthold to be one of the weakest raids Blizz has put out. Infact EN was painfully average too. I think they certainly dropped the ball when compared to BRF / SoO etc. The encounters in NH are just so bland.
1.) The stamp boss, where people got stamped to death. Was hilarious during progression.
2.) Train boss, once again something different (maybe not the add aoe, boss mechanics) but the theme of fighting in the middle of a busy station.
3.) Blackhand-> Hulk smash!! break the dang room.
Heck even HFC had some nice bosses, like socrethar, mannoroth was epic setting (nothing compared to BRF though).
Throne of thunder was golden
1.) Encounter design with having to fly between nests..
2.) A very GOOD council fight
3.) Durumu Maze
It is not so much about the mechanics of the fight itself, but more of the encounter setting. That is what OP is getting at.
Brf Had innovative encounters with trains, ships, blackhand and stampers
ToT had nice innovative settings with Ji kun flying (granted, it was taken of firelands flying), durumu maze
HFC had somewhat with mannoroth (again, not the mechanics) but the encounter settings
Granted Helya felt a little different than the other bosses ( a bit more like sinestra)
and NH guldan has some nice phase transitions.