Blowing the doors off what came before
As much as I think Naxx gets a bad rap nowadays and certainly accomplished what it was designed to do, it's fair to say that in pretty much every way, Ulduar pushes the bar higher. The instance itself when it released was absolutely striking and distinctive, taking art elements from old instances like Uldaman and totally updating them. There really is no comparison between Naxx and Ulduar from an art design perspective. The encounters were well designed, often challenging, and each succeeded in emphasizing different mechanics. Those fights that had hard modes unfolded in organic ways that made sense, whether it was simply killing the Iron Council in a different order or breaking XT-002s or even pushing a clearly marked "Do not push" button in Mimiron's room to work on Firefighter.
Furthermore, achievements in Ulduar felt far less punishing and far more organic. The instance was clearly designed far more naturally to take advantage of them and make them worthwhile, challenging and even sometimes fun without being the ridiculously unforgiving ones Naxxramas offered. Compare Conquerer of Ulduar with The Immortal.
Blowing the doors off what came after
Yes, I'm fairly happy with my certainty here. Ulduar is simply far, far more enjoyable than Trial of the Crusader/Grand Crusader. The art design isn't even comparable (a sprawling titanic city prison for an Old God versus a round room?). The fight design for Ulduar is far more interesting that almost every ToC fight except possibly Anub'arak (and I'd definitely put both Yogg-Saron and Algalon ahead of Anub for challenge and fun). ToC's hard modes are basically far less organic than those of Ulduar. Furthermore, I generally find the Ulduar hard modes to be superior to the conceit of running the exact same instance up to four times (10-man, 10-man hard, 25-man and 25-man hard) with minimal changes and no real explanation for why it's suddenly harder.
If it's fair to say that Ulduar took on a bright shine for many raiders after coming out of Wrath's introductory content, it's also fair to say that the release of patch 3.2 ultimately led to Ulduar taking on an even brighter shine of reflected glory in comparison to ToC/GC.
Making use of existing lore, creating new lore
Frankly, being tangential to the developing story line of Wrath of the Lich King works very heavily in Ulduar's favor. Ulduar as a raid instance is very heavily tied into the lore of Uldaman, Un'Goro Crater, Ahn'Qiraj and the long-established titan/Old God conflict. At the same time, it establishes the existence of the watchers, servants of the titans who worked to shepherd Azeroth and protect it from Old God influence. The existence of Yogg-Saron helps contribute to the story of the Lich King by providing a source for the strange material he uses to construct darn near everything, as well as providing a rich resource for future stories in unfolding titan sites like Uldum. Furthermore, the presence of an actual Old God of Death working against Arthas/The Lich King has all sorts of possibilities. It's fairly clear from the Yogg-Saron fight itself that ol' Yoggy was tipping us off to Arthas' plan for Bolvar, and it wouldn't surprise me at all to discover that Old Gods like C'thun and Yogg aren't so easily slain as all that.
Also, Ulduar contains the ultimate in high stakes. Yes, if we fail to stop the Lich King, he'll continue to try and destroy or subvert all life on Azeroth, and while the idea of a cadre of heroes like, say, you and your fellow raiders as servants/soldiers of the Scourge is indeed very bad news, even that has a hard time topping the idea that if you don't beat Algalon in one hour, Azeroth and everything on it will be broken down into component elements and recreated from scratch. There's simply no way around it. The stakes here are as high as they have ever gotten in WoW -- and the best part is, if you have ever run the Halls of Lightning, it's possibly directly your fault that the world is about to end, because you killed Loken. Killing Loken, Yogg-Saron's enslaved prime designate among the titanic watchers, is what activated the Algalon Protocol in the first place.
In the end, Ulduar took what had gone before it and very handily separated the wheat from the chaff, and then made some really awesome bread out of that wheat. (I just did irreparable damage to that poor idiom; I'm a monster.) It either improved upon or created everything we currently enjoy in raiding and was, by virtue of its freedom from the overarching plotline of the expansion, totally able and willing to create awesome new antagonists for us to murder for loot. It is definitely a candidate for best raid of this expansion.