Samsung has improved the software to go along with the S Pen too. You can now hover over an email with the pen and see the first sentence of the message, customize what app pops up when you start writing on the screen, and still use Samsung's S Note, a combo note-taking and sketching application.
And if you're worried you'd lose the pen, Samsung's come up with a solution for that. The phone will alert you with an alarm sound if the pen has been left behind somewhere.