Gregory, the problem with your position is the fundamental assumption of bad faith that runs through so many of your arguments. Whether it's Creative Commons 3.0 or a collaboration with the Archive, other organizations are always insufficiently committed to freedom and therefore impossible to collaborate with.
The problem with this kind of free culture isolationism is that dogmatic blindness achieves exactly the opposite of what you are hoping for. It will lead to other projects which haven't spend a minute even thinking about the implications of copyright and file format policies becoming dominant, simply because they choose to adopt mainstream technology and put ease of use before anything else. It will lead to us being overwhelmed and understaffed as we refuse to accept help from anyone who isn't already carrying the same flag we are carrying. We need balance and reason, not dogma and hostility.
Creative Commons, the Internet Archive, Mozilla, and others are very valuable institutions of a broadly defined movement towards making terabytes worth of cultural works available online, reducing barriers to access, providing freely usable & freely licensed tools, developing sane legal frameworks, and so on. I, too, would prefer it if these institutions would generally advocate similarly high standards of freedom as we do, and where this is not the case, I generally try to persuade them to do so.
However, that does not negate their efforts, nor does it mean that we should avoid working with them. We should try to help them when we think they could do better. We should treat them as potential friends and allies, not alienate them with a priori assumptions about their motives and their direction.
Case in point: You argue that the Archive is not a suitable partner because they are currently not supporting Theora. Well, they are already supporting Vorbis for many of their audio collections, and according to Brewster, the main reason for the lack of Theora support is quite simply that there has not been substantial demand for it so far. We, as a partner, could make it quite clear that Theora is a requirement for a collaboration around video hosting. Indeed, I already said as much to Brewster, and he signaled that adding Theora support to their transcoding pipeline would not be much of an issue at all.
If you want to effect policy changes in other organizations, you need to start talking to them! A partnership with WMF would push them towards adopting free formats, because it would be an implicit requirement for such a partnership to happen. Similarly, their Terms of Service were last updated in March 2001, before Creative Commons and others even existed to raise awareness of the importance of licensing and content freedom. I doubt that anyone but the lawyer who wrote the thing even has looked at it since then. Have you tried to send them feedback about it? Once again, _talk_ to people, don't just condemn what they are doing.
It's exactly the same with CC 3.0 and many other issues. Your stance tends to be: "No! These people are doing bad things! We should stay away from them! Don't you dare talk to them!" My position is: If we want our ideas to spread, we need to reach out to others and _convince_ them, not condemn them, as part of the process of collaboration. And, if that process goes both ways, and people in our community are convinced that they are sometimes too militaristic about certain issues, I don't think that would be unhealthy or unhelpful at all.
Yours is a position of rigid, dogmatic isolationism -- not one of open-minded, thoughtful outreach. That's regrettable, and I do not share it, and intend to continue talking to others, listening to them, and trying to reason with them instead. Wikimedia needs to go beyond navel gazing and self-paralysis; it needs to continue to reinvent itself and work with others in achieving its mission of building a global, free culture and achieving free education for all.