Ajax and moderation will be hugely valuable! I echo the others who have thanked Gideon for developing this project.
HTML Templates - I have spent about 2 weeks, full time, customizing Q2A to fit my site's particular needs and the biggest portion of that time has been dealing with themes. Currently, layout is determined within the structure of theme functions, which makes it hard to do simple things like "display the upvote button on the left of the question and the down vote button on the right". Silly example, but you get the point. Both buttons are included in a single larger function (qa_html_theme_base::voting) that assumes they will always appear together. Changing this default behavior is not easy. It would be so much faster to have HTML templates so that I could edit the structure of the markup without worrying about. For the purpose of bringing Q2A forward to the point where it can achieve really wide adoption, I think this is the most important thing you can do.
Featured questions - Formspring.me has gotten great user engagement from "Questions of the day" that they write and feature on the site and in daily emails to users. I think this could be a powerful way to help Q2A sites grow. In the early days when there are few questions, this can give people something fun to do on the site.
Act as Admin - I would like to be able to take actions as the site itself. This would help provide consistent branding and would fit nicely with featured questions. Formspring.me also does a nice job of using this technique to provide an "official" feel to certain activity.
Avoid Global variables, use Classes / inheritance to make Q2A more extensible - Global variables make it tough to integrate Q2A into existing sites. It's also tough to tweak the behavior of particular functions that aren't in the themes. There is no way to easily overwrite them so you have to make inline changes that make upgrading difficult. If everything were in a class that would automatically look for it's extension (as qa_html_theme_base already does) it would be so much easier to hack changes into the system.
Bookmark / follow Questions & People - pretty simple idea
Github - I agree with above commenters that this would help a lot, though I understand the reasons it might not happen.
Also valuable would be:
Badges - there are well-established models out there. The trick would be to make it easy for developers to write their own criteria for new badges, as you have already done with titles. (The difference is that titles replace earlier titles, whereas badges accumulate)
More email tools - As an admin, I would like to be able to email everyone who is involved with a question. Others have had good suggestions here too.
**EDIT**
Location tags - I think location tagging could also be extremely valuable for many Q2A sites. Ideally, we could auto-tag questions with the user's location (which would be part of the external users integration) but also allow people to change / modify the location tag for a given question. Facebook has started doing this for status updates and it is generating a tremendously valuable dataset for them.
