Vanilla had the super-long instances, which while full of awesome, were frequently too long for the average player. BRD was probably the peak of this, though Mara and LBRS weren't exactly short.
BC had... hallways. Some were even very short hallways like the Mechanar. Then there were the woefully non-labyrinthine Shadow Labyrinths. Don't getme wrong, BC instances weren't terrible. They had their moments. Who can not laugh at the dialog between the demon bosses in Arcatraz? Oh, and Millhouse, good stuff. Still, they were a bit dull to run, lacking anything at all to explore or discover. There was no sense of scale.
It's not that linear instances are innately bad. They just have to be done well. UBRS was linear, and yet it was one of my favorite instances. Shadowfang Keep is perfectly linear but the way it is laid out gives a sense of being a little castle, a real building, rather than just an aimlessly wandering path. SFK is probably one of the best instances in vanilla.
WotLK instances are simply amazing. They're not huge or complex to navigate. In fact they're mostly linear. But the way they are set up gives a great sense of scale. Just today I was running through Gun'drak when I looked to my left just past the snake boss room and just stood there. I was awestruck by the vast scale of the temple/fortress we were in.
WotLK instances have a ton of 'wasted' space: areas that we will never run into and never need to know exist. But these areas give the scale that was missing in BC. Ahn'Kahet and Azjol'Nerub both have large areas of wasted space and they make good use of them. The first makes you feel like you're in the middle of a city. It almost felt like in BRD when you look out over the lava and see all these homes carved into the distant walls. AN is less extravagant with space, until you do the drop before the last boss. You go past several levels of carved out city, packed with spidery architecture. After that you can't pretend it's just a hallway: you're in the heart of the Nerubian civilization, or at least the part conquered by the Scourge.
The heavy use of open sky also helps. It reminds us that we're not in some isolated bit of hallway, we're still in the world and we can see it. I'm not a huge fan of DTK, but near the end when you're doing the troll-undead pulls along that balcony, look to the left. See a troll civilization out there. Utgarde Keep makes good use of open air as well while Utgarde Pinnacle uses it sparingly, to show not the sky, but the holes in the roof and the decay which is brought by Scourge influence.
It really feels like Blizzard brought out the greatest creativity they could when creating the WotLK instances. They're practical to run, being 30-90 minutes, but give a large sense of scale and a place in the world. You can almost forget you even went through a portal. That is one of the biggest signs of a well-designed instance.