Firstly, just wanted to say thanks for all your hard work on Q2A so far! OK here goes:
1. On-site notifications
In other words when a user comes back to the site there can be an icon by their username showing they have new answers on their questions or comments on their answers. Click the icon to show all replies (new ones maybe highlighted in some way). Similar to reddit or stack overflow. I would rather use that and see a list of replies instead of getting constant emails.
2. Points-based permissions
I think for this you can add a box on the right of each line in the current permissions. So you can now enter like this:
Adding questions: [Registered users] and at least  points
Voting down: [Registered users] and at least  points
Posting links: [Registered users with email confirmed] and at least  points
Hiding any post: [Moderators, Admins] (points box gets hidden here)
You will probably need to be more fine-grained in the permissions, eg separate up and down voting permissions and decide if there are any useful new ones like "posting links", "creating new tags" etc.
3. A good spit-and-polish ;)
It would be nice to work on some of the usability a bit more. For example, showing comment/answer forms immediately instead of needing a whole new page load. Currently if you are not logged in, you click "Comment" and a new page loads telling you you need to login in...then you gotta click "Login" to load another page, log in and come back to where you were.
I think now is the time to switch to something like jQuery to make it really easy to do AJAX, DOM selection, and showing/hiding forms.
4. Edit history
Being able to see edit history would be useful so that the OP can see what was changed in their post and maybe roll it back if they like. Stack Overflow does this well.
Since no one else has mentioned it this time, I'll put in a request for badges/achievements. They are not vital for me but I think they would be a fun addition (especially for a gaming site like mine). See my recent answer for a suggestion on how they could work.
I originally put this at #4 but then remembered something more important. I would love to have multiple sessions. In other words, when I click "Remember me", it should remember me! And not log me out if I signed in on a different computer. (Also, a button in the user's profile to "sign out of all other sessions" like Gmail has would be cool.)
Oh and hopefully you'll move all content output into the base theme class :)