Moxie Marlinspike asserts that federation needs standardization and that standardization inhibits changes. He also asserts that protocols have to change to keep up with changing requirements. His unspoken assumption is that it is impossible to create real-world forward-compatible protocols.
While I agree with the first assertion, I strongly disagree on the latter two. Consider that protocols and data formats that do not have to change exist. An encoding like UTF-8 will probably never have to change to keep up with new codepoints. Also consider that forward-compatible protocols and data formats exist. HTTP seems to be a very good example for that.
I believe with enough traction, we could get hedge funds to give money while shorting the publicly traded companies that operate walled-garden networks.
N.B. I read your link when it was written originally, and have not taken the time to go at the issues raised point-for-point, but I'd like to see more efforts made in the direction I mentioned above.
Edit: The protocol has to have federation built-in from the beginning, and the ability of any server to granularly discriminate against any given TLD at their operator's discretion.