You know, I was using the digital inking/sketch feature in Evernote today with my pencil and it's truly great - the tools are good, natural, they have good smoothing and pressure sensitivity, and the results look good.
I just wish the PDF markup would look like the digital inking, rather than the outdated ex-skitch pink crayon stuff. Just make the markup mirror what already exists in the digital inking capability (maybe with a text tool) and I'd be over the moon.