Sorry, but a lot of the advanced organization features for VS2005 projects just aren't supported yet. Rather than take the chance of ripping the project file to pieces, we decided to disable some of the hierarchy editing features. We were able to sneak in support for reading the new "virtual sub-folder" structure of the top-level solution items folder, as well as some support for the new website solutions that don't actually have any project files in them. But VS2005's new freewheeling organization architecture breaks quite a few of the rules and assumptions that have been made over the years.
So that being said, what features of the new structure are you taking advantage of? We certainly can't get everything in, but it would help us to know what features should go on top of the stack.