The Apple Pencil is one of the key “value adds” that the iPad Pro range of tablets has. It helps promote the hardware as suitable for creatives, increases the use of the tablet to author new content (as opposed to being used to consume content, a role that historically tablets have been very good at) and also keeps Apple relevant in the small but fanatical “pen-based computing” circles.
Any hardware changes will probably focus on charging and internal hardware or a new innovative design change that Apple will use to wow the audience with. According to most analysts it makes sense to update the Apple Pencil and make the potentially new iPad Pro with a 10-inch display. While the pencil may not be used by every consumer, it is greatly appreciated by those who do.