Chris Welch received an official statement from Apple regarding navigating the UI with the Apple Pencil, which I mentioned recently:
Apple Pencil has been a huge hit with iPad Pro users, who love it for drawing, annotating and taking notes. We believe a finger will always be the primary way users navigate on an iPad, but we understand that some customers like to use Apple Pencil for this as well and we’ve been working on ways to better implement this while maintaining compatibility during this latest beta cycle. We will add this functionality back in the next beta of iOS 9.3.
This is good news. Whatever the real reason, I’m glad it’s here to stay.