I really didn't like Avenue Q at all, but it was very original and consistent in its originality. I really liked Caroline, although I actually thought the score was weak.
I loved Wicked, but I didn't (and still don't) actually think it was very good. The direction was awful, there were a number of scenes that stopped the action entirely, and did the sets and costumes really have to be that ugly? On the other hand, the basic story was compelling, the score included 5 or 6 terrific songs that people LOVED, Idina and Kristin were wonderful, etc.
I have always thought that the inconsistency in Quality in Wicked lost it the Tony. Went from really excellent / outstanding (Popular, Defying Gravity, the big number in the Emerald City led by Fiyero, For Good...intermittent cleverness focused on the basic conceit of the show) to terrible (most of the scenes with Madame Horrible and the Wizard, talky and / or mediocre songs).
Of course, it may also be that they simply thought the win for Avenue Q would increase the likelihood that it would be successful on the road, which Wicked was by now guaranteed...of course, that was an entirely different story.