Bornakk chimes in to say that The Burning Crusade dungeon design was heavily influenced by player feedback, wishing for more Scarlet Monastery-esque dungeons. I can see that, and to an extent, I agree with that, too. Scarlet Monastery, while shorter and more linear, was also pretty cool.
Personally, I don't think that it really comes down to one or the other. Take Dire Maul, for instance. Each wing could be tackled in a straightforward, linear fashion. However, each of them also had alternative routes, and some of them even had alternative ways of defeating them. For example, Tribute Runs in Dire Maul: North. Plus, they were even connected via the library. If you really want to, you could go from one wing to the other without any loading screen.