I have updated to Visual Studio 2013 update 2 and now I cannot scaffold controllers.
The problem is not project specific: when I try to scaffold
I had the very same issue with Visual Studio 2013 Update 3, but only for the scaffolders working with Entity Framework. The issue is seemingly caused by the incompatibility between Entity Framework 6.1.0 and the scaffolders in Visual Studio 2013 Update 2 and above.
To upgrade EF do the following:
Uninstall-Package EntityFramework -Force
Install-Package EntityFramework
This answer is borrowed from here
After the upgrade the scaffolders are working fine for me. Make sure to install the new version in every project where Entity Framework is required.