I've been following Scott's progress with the Web Application Project (coined WAP) for some time now and after converting my pet project over to ASP.NET 2.0 and finding the problems with the new VS2005 IDE I was greatful for his work! The download is on MSDN.
The biggest one for me was definately the locking of .aspx files when in debug mode and the batch compilation it does without the new .designer.cs files that are in this new project.
I've found a few errors mainly regarding where .cs files have to sit. The main ones were 'ambiguous match found' where a control was defined in multiple places in the .cs and the designer.cs files...thanks to stevienova.com for the resolution of this one.
For some reason though ti appears that one of my class files is being included in the WAP .dll file as well ans when it compiles the app_code at runtime.

error CS0433: The type 'inlinehockey._common' exists in both 'c:\WINDOWS\Microsoft.NET\Framework\v2.0.50727\Temporary ASP.NET Files\root\25321638\9b5c4b00\assembly\dl3\3657f4e6\cd91aef5_4d5cc601\inlinehockey.DLL' and 'c:\WINDOWS\Microsoft.NET\Framework\v2.0.50727\Temporary ASP.NET Files\root\25321638\9b5c4b00\App_Code.xad_ajc1.dll' 

The error was not knowing what dll to use for the type when you get the CS0433 error. I found out how to get round this from the microsoft.com upgrade experience, but it didn't solve it for me. I've posted this up in the forums...hopefully I'll get an answer!