I know it sounds like Nintendo defence force (for the record I thought Nintendo completely botched E3, and I don't think the Wii U will do very well, though I'm still interested in its potential), but I honestly believe a stylus is more important to gaming applications than clumsy, inaccurate capacitive multitouch.
A stylus allows for custom art/textures, for precise RTS commands or map editing, doesn't obscure nearly as much of the interface, etc.
For certain apps, like Draw Something, I *wish* my Galaxy Nexus could use a half way decent stylus (capacitive styluses generally suck, are ridiculously expensive, and many of them wear out rather quickly).
Yes, capacitive is great for smartphones, for something that's in your pocket that you need to interact with in brief spurts in crowded spaces, but for GAMING I've found it's usually less than ideal.
EDIT: Of course, if Nintendo wanted to spend a shit ton of money they could have gone with an active digitizer + capacitive, which would mean the best of both worlds, but I suspect that would have been at least twice the price.