All you have to do to register an MVC widget is add a 'ControllerToolboxItem' to your controller.
[ControllerToolboxItem(Name = "Home", Title = "Home", SectionName = "MvcWidgets")]
Like I mentioned, as long as you leave the default 'SitefinityWebApp' namespace in place, it works perfectly. But when you apply your own namespace, MVC widgets fail to register.
I'm familiar with the MVC only templates. That's not the issues.