One advantage that Samsung's S Pen stylus has always had over the Apple Pencil is its ability to tie into Samsung's software to enable certain shortcuts and features.
With iPadOS, it looks like Apple Pencil owners will get a small taste of this type of functionality, too. You'll be able to take a screenshot in iPadOS by dragging the Apple Pencil from either bottom corner of the screen. While the Apple Pencil is still largely intended to be a tool for drawing, sketching, writing, and annotating rather than user interface shortcuts, it's refreshing to see another use case for Apple's stylus.
Other than the new screenshotting feature, the Apple Pencil will be capable of working at a lower latency thanks to Apple's improved prediction algorithms.