What we're doing is as follows:
We're ignoring the iPad specific storyboard that Xcode sets up for us.
We have a single storyboard for both iPad and iPhone. So far ALL the scenes are shared between them. If we need to create a custom scene for iPad at any point, we'll create a separate scene and give it an identifier with the suffix _iPad. Then we'll write code to load that at runtime. (The app uses a scheme where it instantiates view controllers from a descriptor file, and uses unique IDs instead of segues.)
Storyboards are the wave of the future. Many of Apple's new tricks are built on storyboards, and don't work with XIBs, or are much harder to use with XIBs.
As a simple example, iOS 6 has embed segues, which make it PAINLESS to create parent/child view controller relationships. Without that, you have a fair amount of rather fussy code to write. Certain view controllers like table view controllers pretty much have to be child view controllers (since a table view controller's root view is a table view, it doesn't lend itself to managing other UI elements)
I put off learning storyboards for quite a while, and regret that I did.
http://www.agileinfoways.com/technical-expertise/mobile-applications-development/iphone/ Overall they are easier to use, enable new features, and are well worth it. I was productive with storyboards almost instantly.