I upgraded my Web API app to the funkelnagelneu versions using this guidance:
http://www.asp.net/mvc/tutorials/mvc-5/how-to-upgrade-an-aspnet-mvc-4-and-web-api-proj
In the last step on the migration guide did you delete only the MVC4 Project Guid that is specified? I had the same problem as you and when I retraced my steps realised that I had deleted all three of the Guids within in my .csproj file. I restored the other Guids within this element and the solution now recognises it as a MVC application and now works OK. So the line now reads:
{349c5851-65df-11da-9384-00065b846f21};{fae04ec0-301f-11d3-bf4b-00c04f79efbc}
Hope that helps