Things have significantly changed in BizTalk 2009 opposed to BizTalk 2006 regarding to the Visual Studio project structure. BizTalk 2009 is now a first class citizen of Visual Studio so there is no longer a special BizTalk BizTalk project structure. The
BSF is targetted at Visual Studio 2005 so it won't work with Visual Studio 2008 as used for BizTalk 2009.
Besides that, the GAT/GAX which are used to build the BSF are different between the Visual Studio 2005 and Visual Studio 2008 versions.
At this moment there are no concrete plans to migrate the BSF to Visual Studio 2008 using the current code base, but if you like to dive into this I would encourage it.