First, I'm not a developer, I'm just a fan of Q2A and its developers (Gidgreen, Pupi, Sama and others). I have learned a lot from Q2A despite not having any knowledge of programming or development sites. So I just have to hope that the project proceed and wish success to PowerQA.
Now, some suggestions, sorry to be bothering you :)
Notifications on the site should be part of the core and not plugin.
This wonderful answer of Pupi too: http://www.question2answer.org/qa/46629/
I also think, to modify and customize the order of the menu and submenu at the core, is needed. I've seen users asking to "pull" forward "ask" in Q2A.
Button answer more visible, as in SnowFlat theme would be interesting too.
"related questions" should have an option to display the latest questions in a category or with the same tags.
Wonderful widgets Sama (My Followers, Follow Users, questions followers), they should be used. I would not use Q2A without using them.
Finally, the category list on the side panel must be removable in a few pages.
I know that all I said, you can do with plugins, hacks or widgets, but become Q2A or PowerQA most complete in the core.
I forgot a very important thing.
Do not allow any user to edit the question title. This I think the most important among the missing in Q2A.