What you are asking to do makes sense, but is not available out of the box. You can override the T4 templates, with this command
> scaffold customTemplate Controller
But to work across projects, you will need to dive into the powershell and create your own scaffolder
> scaffold customScaffolder ViewModel
See Steven Sanderson's blog posts for more information. Also see this blog post for help in generating DTO or POCO classes in T4 templates.