Thanks to this thread I have identified a couple of issues with the Routing. In part, was my original assumptions turned out incorrect - I thought the two philosophies would be used separately. Either you had a namespaced controller that was specified in the routes file, or the auto-routed version to stuff in the controller folder, where the classes were in the global namespace.
Listening to your feedback, I've gone back and fixed one issue that was keeping non-namespaced controllers from being auto-routed last night. Though I'm trying to find a nice way to make it testable currently.
And I will be working on making auto-routing working with namespaces - as long as that namespace lands in the controllers folder, anyway.
So - thanks for the feedback! And, have patience, we'll work the bugs out.