Yes, Wrath had flaws, but Wrath was still the best. Especially at the time it was the peak of MMO gaming and the end game was alright. Most of the player base had finally reached a skilled level, compared to Vanilla and BC where the common player was pretty garbage. The Community was at its peak at this time as well and servers were pretty thriving places without cross realm stuff. Until the second iteration of LFD showed up, originally it was server wide only before becoming battle group.
I'm not going to wax on about the questing, because yes, questing is the one thing we can all point to and say, "Yes, it is way better now than ever." A lot of that has to do with the tech at the time and new mmos and RPGs generally creating better quest systems.
Zones, yes you could fly over a lot of stuff, BUT that was because the world was supposed to feel like an epic war was taking place on the entire continent, especially near the epicenters of that evil, Ice Crown and Storm Peaks. So the idea of flying over it was to give you a sense of this never ending battle going on, running through that wouldn't have the same effect.
The story was fairly predictable, but it was supposed to be, this wasn't some new evil showing up or some sneak attack by someone in hiding, it was a guy we've known about and who had been attacking us since WarCraft 3. This was a "Look over there, see that dark spot that is where the bad guys live. It is time to go put an end to this." Story line and it was pretty well handled. With the 5mans leading up to it, the story of the titan discoveries through raids and 5 mans. I found Wrath to really open up the Warcraft universe lore a bit, before that we had only had suggestions to some of that stuff and now we were seeing it and discovering it and the lore was growing.
Old Gods have been middle tiers, it has been a thing. Ulduar is a great raid, was a great raid, never felt shoe horned, and had some badass ground breaking stuff that lead to modern raiding. It also had some great lore discoveries and brought about an entire section of the Keepers, Old Gods, titans etc. To just wave a hand and dismiss it because it was the second tier is well, dismissive.
Crystal Song, like Zul'Darak, did meet with a sad fate. But at the same time Dalaran was over crystal song and we really didn't need to be parked over the war itself, but centrally located. I'm going to stab at there was going to be some tech problems had Crystal song been a thriving hub, as well, with Dal above it. But again, it is sad that both those zones didn't see more.
Overall Wrath is the best expansion for a lot of reasons and some of those have to do with time and tech as much as the content of the game. The growth between Vanilla/BC and Wrath is impressive in all facets of the game: Design, Lore, Community, Raiding, 5 mans, various endgame content, and PvP. Wrath laid the groundwork for the modern era of WoW, which I really love and I've been around since Vanilla never unsubbing. We nit pick expansions a lot, but really the game is still good and Wrath shows the peak of blizzard in the MMO community.
Calling the Wrath the best expansion means more than the sum of its content. Was cata better? Only the questing, everything else in Cata was pretty much copy paste and moved the game very little forward, MoP was much better and moved the game forward. WoD questing was great, some solid raids, but otherwise it was pretty lacking and they know that. I have high hopes for Legion coming very close to Wrath, but we'll see.
Wrath had flaws, but it doesn't stop it from being the best expansion. And there is a lot of outside forces that made that happen, not just the content of Wrath. If Wrath isn't the best which expansion is? And also, the only flaws you found were basically quest based and an empty zone.
Take for instance, Doom and Doom II are revered as some of the best FPS of all time. The reasons aren't the content itself was great, but that they were the first 3d and multiplayer FPS games. They basically created a genre. Wrath is kind of like that, it was the turning point for MMOs and pretty much capped WoW as THE mmo.