First of all I must say that the ASP.NET team has created a lot of great things with version 2, but in my mind they have really failed with the new project structure.
First of all I don't like that the project dialog has another structure than for all the other projects. I can't see why developers have to learn two different places to find the same settings? I haven't find where to set up conditional statements (other than DEBUG and TRACE). Our biggest hassle though is with the fact that all files are part of the project and therefore is checked in to SourceSafe. First of all I don't like that I can't control what is checked in, and what's not. This means that files that we don't want to be in SourceSafe must be there. One example of this is that we have used the possibility to have a local file for the appsettings and some of our own parts of the config file. We used this to be able to control for example which database the developer used when debugging or testing. Now all get the same file.
I also have some minor things that I don't like, but those is more of my personal preferences. What is great though is that I found out that the ASP.NET team is working on a new project model that will be more like the 2003 version with a project file and more. This will probably solve many things that I don't like.
Read more at Scott Guthries blog.