Apparently I'm not the only one who's hearing the buzz around the new web projects in Visual Studio 2005. Scott Guthrie is too. And he's on vacation in Mexico!
Anyway, he has a great post explaining a few things. Both of the issues I listed earlier (references and excluding files) are handled in post-beta builds, something I wasn't aware of. Here's another example of Microsoft listening to what the developers want.
Seriously though, with a guy like Scott running the ASP.NET team, you knew there had to be a solution in the works.