If an app doesn't implement the Pencil SDK it is nothing more than a precise mechanical finger. I'd love to be able to use the Pencil also in apps which don't support it. Allow me to annotate everything, everywhere and give the OS a sort of memory layer of all doodles I place everywhere. I'm currently typing this in Ulysess, my favourite writing app which doesn't make use of the Pencil. I'd love to highlight certain sentences, cross out certain things and make small doodles in the sideline.
Let me doodle OS-wide; on top of app icons, photos. I don't want to wait on the app developers for support of the Pencil. Adding an annotation layer to iOS itself would turn this iPad into a true "bicycle for the mind".
Allowing users to doodle on the OS-level turns the whole system into a canvas for thinking.