I get all this by not using github. Minimized comments: I run the mailing list and can enable moderation at any time. Retire namespace: I control the web server and so every aspect of the URL after the domain name. Unwanted pull requests: no different from unwanted anything else.
Downside: Holy shit fuck mailing lists. They're terrible . Major downside: You miss a huge percentage of possible contributors.
What do you find terrible about them? When browsing email lists like the one used for developing git itself, I find it very easy to go through various patch sets and follow the discussion they have on each commit. My client makes it easy to search for subjects, expand or collapse threads, search for authors, etc.
The emails themselves are easy to read and don't require an excessive amount of scrolling to go through even if the patch set has multiple commits. It's quite easy to see comments on a patch set inline with the patch itself.