This is kind of out there, and more of a long term project for when/if the site gets out of beta and I'd be more than willing to help out with the programming.
What I'd like to see is the ability to make questions in the style of St. Thomas Aquinas's Summa Theologica.
The reasoning behind this would essentially be to control the conversation and not make all our contentious questions be asked by atheists.
The initial question would be some sort of theological hypothesis:
It would seem as though women should not have beards in Heaven
People could answer with their objections
Women should have beards in Heaven because they prefigure Christ
(objections would be downvoted, but the most downvoted answers would actually rise to the top by default)
People could answer with their supporting statements
Women should not have beards because their nature is still female.
Replies to objections would be comments in the objections. This would also give people opportunities to write objections to supporting evidence, unlike the Summa.
When an answer is chosen, the original poster gets an opportunity to write an 'I reply that...' statement and an 'in conclusion' statement, which would go in between the objections and supporting evidence and on the bottom of every page in the post respectively.
I think this would be a better way to ask questions like "Does same sex 'marriage' hurt society?", questions like this don't need to be asked by those who believe it, but we can't let those who have preconceived notions on the issue frame the debate all the time.