The possibility also remains that Wacom did not want the kind of business that the Surface brings to them. The surface is the first product that does a reasonably good job of cannibalizing cintiq sales. I would expect their margins on Cintiq to be higher than selling a digitizer component to Microsoft. I think Wacom is in a really tough place here - they have to balance between limiting access to their crown jewels while also making sure that ntrig doesnt make too many inroads as a legitimate alternative.
Absolutely nothing to do with that. Wacom would love to be in the SP3. But weight, thickness, cooling, display quality (and writing feel due to extra layers between the glass and display panel), and battery life all conspired against them. The N-Trig solution trades off some drawing precision (at a degree very few will notice) and the requirement of a battery in the pen for improvements to all of those things. Seems like a no-brainer.
When I was at MS folks were working super closely with Atmel (touch panel vendor for most early Win8/RT tablets) and really pushed the limits of their technology. There was a tight feedback loop there and I personally had found issues which eventually were solved via iterations of back-and-forth with Atmel and with software tweaks to work around hardware limitations.
It may not happen over night, but I suspect they're doing the same thing with N-Trig and pushing them to improve the experience in a way which other PC/tablet vendors never have or would. So don't assume that just because other OEMs haven't cared enough to get the most out of N-Trig's text that Surface doesn't have a shot at doing better.