The most recent beta of iOS 9.3 has removed the important functionality for the Apple Pencil: the ability to use the stylus accessory as a finger replacement to select options and menus in apps, swipe between apps, tap on buttons and use the Pencil for general navigational purposes throughout iOS.
If Apple does not change its mind and re-add this functionality in a final version of iOS 9.3, people who rely on the Pencil to edit content on their iPad Pro will be forced to use their hand to select tools in apps like Pixelmator, for example, marking a major usability regression.
As first noted by MacRumors, the disturbing feature removal which limits the Pencil's functionality has enraged users who have grown accustomed to using the stylus for navigational purposes.