To me the storyline in the expansion was a letdown. They build up the characters so much during each race's campaign and fail to followthrough on the climax. They do an excellent job of getting you emotionally involved in a couple of the main character's plotlines but the ending leaves you wanting more detail and richness. Also, I was a big fan of all the cutscenes in the original WC3; there are a total of 2 in the expansion, everything else is handled in-engine. The first cutscene is great visually, but the dialog is lamentably campy. The end 'finale' cutscene comes off as being tacked-on, unfinished, and not-quite-ready for primetime.
* Edit: I have the same sorts of problems with the newest Harry Potter book and I think the culprit could be the same thing in both cases: Lack of strong editorial influence.
I don't want to sound so negative, however. The expansion is a must-have for gameplay alone. The maps are very much improved from the original... I think there are only a couple maps where you start with a small base, expand, and attack... the rest are more along the lines of static forces invading an installation, and other quest-type pursuits. There are even a couple maps which mirror some of the more popular player-created maps you see on the various fansites. The new units seem very well balanced and just plain feel cooler. AI is incredible... on the "Hard" setting it plays better than 95% of my online opponents.