One of Stack Exchange's weaknesses is inter-stack collaboration:
If a question has the tags "Math" and "History" why should the same question, comments, and answers not appear on both the Math and the History sites? Comments from the historians would surely be welcomed by the mathematicians and vice-versa.
Asking the same question on two different sites currently results in one of the answers being overlooked-especially if the viewer comes from a search engine.
Area 51 could be eliminated if a new stack were created for every tag that gets used say 1,000 times per year (or another strategically chosen number) and is approved by a moderator.
The end result of implementing such an somewhat self-morphing system of stacks would look something like a portolan map, with stacks interconnected using tags instead of lines.
Implementing faqs could be trickier than with the current Area 51 system, but a beta period could surely be used for faqs with the people who used the tag invited to the private beta.
Using such a tag system it might even be possible to create a personalized stacks that include user-defined tags/topics. A new user to stack-exchange might be able to select what general topics (science, history, pop-culture, etc., which would include all relevant tags) and even specific tags he/she wishes to be included in his/her own personal stack.