There's one good hypothesis for it that I posted in another thread:
Wacom tech doesn't let you use your finger.
Capacitive tech isn't very stylus friendly.
A good e-reader experience leans on both when dealing with touch. Fingers on EPDs would be painful to highlight things accurately (see the iPhone's UI here...). Stylus navigating around a book list is begging to have the stylus lost, or really just not needed when you have nice big icons.
Sony's really thinking that touch is the future, but in a way they are jumping a little too far ahead on the user experience before tech has caught up to let them do it.
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