I want to end up with a single VS project/solution that I can check in to source control, that any other developer in the office can simply check out and run, and that I can deploy without having to install EPiServer program files on every web server.
I have just used the EPiServer 6 Deployment center (part of the official EPiServer 6 download). That gave me an EPiServer templates project, website setup in IIS, and a database installed.
The first issue is that when I change the VS project file to use the Visual Studio Development Server, the cms start page (site centre) no longer works.
And an even bigger problem is that the episerver.config file is using all sorts of files in the C:\Program Files (x86)\EPiServer directory on my machine.
You can remove the virtualPath items pointing to Program Files in the config file and copy those folders to the same paths inside the source controlled project folder.