Having a pen-dominated UI is also a huge usability mistake. The pen is a great optional peripheral. But UIs that require pens have been rejected time and again.
I almost never use the pen unless I am in note taking mode or doodling in OneNote. There is a certain level of conscious effort required to take out a pen, which limits its overall use. The laptop with touch I find myself tapping the screen to hit links and buttons on a semi-regular basis.
Essentially the pen is super comfortable for a very small niche, but is too big for me to want to carry it all the time. (Its the size of a paper notebook...) I am not the type to carry a moleskin around though, for what thats worth.
Take into account that actual UI are designed for mouses, but there is not such a need. Humans find way more natural to use pens and fingers than keyboards.