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.
Stratholme was also mostly linear. You go in the side you want to do, you kill the bosses in your way, and you kill the boss at the end of that side. However, there were also extra bosses you could do if you wanted to take a turn off of the main road. If you wanted to do the other half of the dungeon for some reason once you've finished the first, you can fight your way over there. It gave these dungeons the feeling of being much larger than they actually were, not to mention more 'epic.' There were a lot of little side quests you could do in addition to the main, linear dungeon.
I don't think the problem is that there are too many short dungeons. The problem is none of them have anything that can be done outside of the norm, like alternate routes you can take or things of that sort. Short is good. Options and side quests are also good. That being said, the Utgarde Keep preview Blizzard gave us awhile back makes it seem like they have realized some of this. The preview mentions additional rooms on Heroic mode and things of that sort, so maybe this has been addressed in one way or another.