Users can arrange NAT traversal or tunnelling as appropriate, and have a better success rate than services which have to anticipate all of the different NAT configurations (and test them), without pissing off users. It's clear that the browser can help a lot here.
WebRTC is deployed on somewhere around 40% of browsers and is potentially supported on some 80-90% of those browsers, and works on maybe half of the services. Your mileage may vary, but there's not going to be a Skype competitor built on WebRTC unless Google makes it and tunnels to Google's servers (which they do).
Requiring servers implement IPv6 correctly is a lot easier than making every server do the STUN/TURN/conntracking dance. It's probably easier than making one server work with WebRTC everywhere, since the only WebRTC app that seems to work for me is Google.
