I'd like to sum several proposals:
1) There should be a bounty award a.k.a. featured questions
2) There should be a personal inbox to aggregate all user related events, especially those events, which engages user to participate in community
3) There should be an option to sort answers by votes, dates or latest activity. To cope with content duplication, rel canonical should be "order by votes" version.
4) Make a visual distinction between ordinary user and real expert is a very good idea. Consider a use-case of some medical consulting site - admins may want to make real doctors look different to present better user experience.
And last but not least thing (IMHO): StackOverflow succeded because they are completely insane about perfect user experience. That means, they are centric at (a) great content, (b) motivated community and (c) site design (not how neat it look, but how good is to use it). You can't do many with a content, you kinda "responsible" for a site engine. And you can do a lot to help build (b) motivated community and (c) site design. Badges, clearly visible user ratings, leader tables, inboxes with "You've just received new badge!" and all carefully selected and crafted StackOveflow's gamification stuff - all of that things should be available out-of-the-box in any SO-clone, that wants to be successfull. Not because SO or Quora also did this, but because it works very well in engaging community to participate.
I've just examined Q2A sites... You know, I'd got bad feeling about I won't be happy using Q2A engine. Most of these sites are overspammed and virtually dead. Could this only be because their owners chose wrong niche and failed to fill their site with a good content and failed to attract vibrant community? Well, eventually yes. But could this be just because they chose wrong site engine, that doesn't engage community enough?...Who knows?
Anyway, thanks for you did to this moment! Wish you luck.
6) User uploaded images should be (or better to say must be) stored at file system. Storing it in a DB is amazingly slow.
7) Overall performance of the engine is slow and should be improved. I was wrong. Posted an answer about it below.
8) It would be nice if the engine will generate absolute URLs (starting with http:// ,or at worst case starting with / if the site is located in root) instead of relative to current position (starting with ../)
9) There should be no invalid URLs at all, it hurts SEO significantly. For example, relative URLs with double slashes are very bad. Mod_rewrite is definately not an option...
10) Please, don't hardcode http protocol version in sources, it can lead to very strange and hard to diagnose problems. Please, use $_SERVER['SERVER_PROTOCOL'] everewhere instead of hardcoded 'HTTP/1.0' or 'HTTP/1.1' strings.
11) ANTISPAM: Moderators should be notified not only about every new question / answer / comment, but when the old one have been edited. May be not everytime, only when new edition contains links to non-whitelisted resources.