So, all over the world, the leading web technologies (Google, Facebook, etc.) are trying to unite all ways of communication under one umbrella; everyone talks to everybody in the same place (and all provide good filtering mechanisms).
Stack Overflow was the same at the beginning, one place to do them all, with tag filtering (and you can probably add another level, say category filtering).
Instead of that, you started to break everything to smaller and smaller pieces (hope you remember, that was the punishment God gave us for building something too good).
Today, when I ask a web question I get answers like these: "this should have been asked in the Stack Exchange site for web development for developers with the letter E in their name." -- That's a dramatization, but to me it sounds stupid, we did this type of thing 14 years ago, the site is still up and running (it is in Hebrew: http://tapuz.co.il/ ) it has a forum for very specific subjects.
So, while you have good community, it is not more then 10-20 people per forum (I guess that for an English site you should multiply this a by several numbers). The point is, people are missing data that way.
Another small problem this caused me personally is: I need to ask some questions in Server Fault, which no one wants to answer without a bounty -- acceptable, I just can't accumulate enough points over there, again, the overall effect is loss of knowledge (I do get my answers else where). Why shouldn't points be transferable, at least for this purpose between sites?
The bottom line is: Make your wonderful system as one as possible, do not try to break it to very small pieces any more.