Is the issue a touring issue? Wicked will tour better. Wicked already plays a 2000 seat theatre, which is around the average seating capacity of most touring houses. Avenue Q plays to a 799 seat house, and fills it wonderfully, It's doubtful it would come across as effectively in a larger house.
That being said, touring bookers only account for 15% of the Tony vote, a far fewer amount than most people think. Could they swing the vote in favor of Wicked? Sure. But you also have to think that just a few months ago, Tony Kushner had a very high profile, critically acclaimed adaptation of Angels in America air on HBO, voters might award him the book Tony as a tie-in to his Golden Globe win... lest we forget that Mary J. Blige, a woman who wrote the line, "No more drama in my life" and who has no connection to Broadway or live theatre, as far as I know, is going to be featured on the Tony telecast in an attempt to get attract more viewers. That said, Avenue Q could concievably take the Tony for best book.
As far as original score, I'm reminded of a very similar situation we had a few seasons back; like now Tony voters were presented with a show from a high profile composer (Mel Brooks) who openly courted the vote for Score, versus a younger composer (David Yazbek) with an original score with a lot of heart. And talk about economics. Although it continues to struggle when Lane and Broderick are not in the show, The Producers is still open. The Full Monty shuttered more than a year ago. Think about the tourists that come here, most of them are not completely up to date with all of the new shows. Having moved here from the Mid-west, I know how difficult it is to keep up with all of the theatre news unless you live here, or you spend all of your time on Broadwayworld, playbill, New York Times, etc. Even still, the average non-NYer is apt to miss a show here or there. When was the last time you saw a tourist at an Off-off Broadway show (not counting a mother of a cast member)? Many tourists gauge the quality of a production based upon how many Tony awards it has won.
Which leads us to the award for Best Musical. Winning the Tony award is extremely important to the commercial life of a new musical. Not only does it increase it's visibility, it becomes the only show many people see. Of the shows that have won the Best Musical Tony in the past 6 years, 4 are still open. Of the 18 shows that lost the Tony award for best musical in the same 6 years, only 2 are still open. I would hope that Avenue Q could win this award, I really enjoyed it. I thought it was something new that was written for my generation (mid-20's) and it's rare that we get such a show. I'd like to see it run for a while.
I could go on, but I'm not sure anyone got this far.
I wish the stage were as narrow as the wire of a tightrope dancer, so that no incompetent would dare step upon it. -Johann Wolfgang Von Goethe