Given that a proposed site is supposed to go through a "discussion" phase, I think there would be a benefit to implementing threaded comments to aid the discussion. It's currently rather hard to follow the flow of different topics of discussion when every comment is just sequential.
[Note - I am specifically talking about the site proposal discussions in Area51. This question is not a duplicate of this or this. I'm not asking for threaded comments in general on the regular trilogy sites.]
The usual argument against threaded comments that "larger comments should be posted as questions" does not work here as the only questions you can post are proposed on/off topic questions for the site, not asking questions or discussing the site proposal itself.