If they had been smart and gone with an 11.6" screen they would have had room to put the pen inside. I almost think that MS did not go with the bigger screen or a port for the pen simply because they had a bunch of Surface Pro cases they needed to use up. This tells me even MS isn't sure this device will sell and didn't want to commit to a full redesign in case it doesn't.
At this price point with an 11.6" screen I believe MS would have sold the hell out of this to business users. Sadly, 10.6" inches is simply too small for a true laptop replacement. Probably a reason all the other hot new hybrids are 11.6" or higher. A bigger screen would also have made room for a larger internal battery and another usb port with a thinner profile.
To me this oversight is a major fail.
I equate the Surface Pro 2 to MS scoring the tying touchdown with a second to play then missing the extra point to lose. It coulda been great, so so close but MS simply does not get it.