Ember logs a warning that transitionTo has been deprecated in favor of transitionToRoute. However, ember currently has route.transitionTo and controller.transitionTo. Only controller.transitionTo has a deprecation notice on the API and in the source code.
Is the notice that route.transitionTo is deprecated a bug, or is the idiomatic method of transitioning changing to this.controllerFor( routename ).transitionToRoute().
ANSWER: NOT DEPRECATED
Turned out I had a mixing using this.transitionTo that was supposed to be involved in route's only but was getting used in a controller, which made it harder to notice.