I think one of the biggest problems of this is that most people when thinking of a five hour wait for Harry Potter consider it in terms of a five hour wait for a Disney attraction, which would be unbearable. What's not being taken into consideration is that this is the most elaborate queue in the history of theme parks. Whereas Disney will throw up a 30 second video game to try to distract patrons from obscenely long waits, check out what Universal has done for Spider-Man, The Mummy and the Simpsons.
What really struck me was one line in this week's podcast, when it was brought up that it's certainly not uncommon for something like Soarin' to have a three hour wait and certainly Test Track and Space Mountain can be at two hours. For the most part, this is hours and hours of doing nothing for a 3-5 minute ride at the end. I'm not knocking the rides, they are all great, but the lack of theming is atrocious. I don't think it's fair to compare a three hour wait for a three minute ride can be to a four hour wait for a one hour "experience."