I have considered moving to the Web Application Project setup that came out. HAve you had experience with this setup (like the old 2003 format) ?
Even tho I have nothing in my App_Code directory, I too have noticed it takes a long time to do the builds.
Web Application Project takes significantly less time to build. The main reason for this is time that takes VS to generate Webform designer classes (partial classes with controls definitions and initialization) in case of Web Site. In case of Web Application Project those files pre-generated at design time and saved to file system. Use WAP to optimize speed up your development process if you willing to let go to some flexibility.