Sometimes the app is not a strict tree of view controllers, but rather a graph containing some cycles. It is here that the whole metaphor of the navigation controller and the visual tools that Xcode gives you to automate it kind of break down and you end up writing lots of hairy custom code to manage your transitions.

Sometimes things are presented modally here but get navigated to normally over there - and once again you're mixing metaphors, implementing some navigation in the storyboard and some of it in code.

I thought the same thing would be true with Auto Layout, but luckily that one seems to have been a bit more "baked" when it shipped, insofar as I've not had any trouble implementing complex views with it WITHOUT ever writing any code.