I’d like to give Microsoft the benefit of the doubt here since they’ve made the rest of the OS so customizable. If you can remove WMP and IE, why should the codecs you use be locked? If the registry values for the codecs can only be modifed by the Windows installer, it’s hopefully just that said codecs will be on the list of removable Windows components once they’ve finalized it.
That’s the optimistic outlook. On the other hand, it may be that this is Microsoft’s last castle, and they won’t give up codec priority because it’s involved in, say, DRM. In that case it would take some more intrusive modifications to allow stuff like x264 to be the default. Well, if that’s the way they want to play it, I think they’ll find the community is willing to do whatever it takes.