Starting with some general comments. . .
Something needed to be done, so kudos for shaking things up. What you want to do with this site requires getting people to act unnaturally in some ways, so structures and incentives to encourage that behavior are probably needed. Even those of us who buy into your goals may need prodding from time to time when things get heated.
As someone trying to participate here, I currently perceive two major obstacles to the site’s success. One is that the noise level has risen. The other is a frequently adversarial stance and a lack of civility. (Aside: in answer to a question I think @Agauger asked, yes, scientists behave this way. Not all of them or all the time, but often enough that it’s a recognized feature of science, and not a good one.) Both obstacles lead to fewer patient, in-depth explorations of arguments and more standard evo/creationist debates.
Some of the problems come with increased size, and I do wonder whether you should be thinking in terms of maintaining a smaller, more focused forum (or collection of forums, e.g. one on theology and one on science) – think Gordon Conferences (but in public view) rather than the annual meeting of the American Society of Whatever with its cast of thousands. Quite a lot of what’s being posted here now seems to have little directly to do with your stated mission and some ruthless pruning might improve the longterm health of the garden.
As for the proposed specifics, they seem like a step in the right direction, although I have difficulty envisioning how they’ll look in practice. There seem to be a lot of moving parts, which is a concern, but maybe all of the machinery will hum quietly in the background. One thing that does seem essential is that platformed exchanges be highly visible, and that it be easy to get from them to the associated side comments.