Comic-Con International posted the following message on the matter this morning:
As many of you are aware, it has been our hope to return to San Francisco for WonderCon 2013. We have been waiting for information on the availability of the Moscone Center and were just officially offered dates, though they were for the fall.
However, those dates coincide with another very large city wide event, and this has resulted in some unavoidable conflicts. Among them hotel room blocks we explored near, and not so near, the Moscone Center started at $300 per night.
This, along with the expected difficulty of exhibitors and attendees in securing airfare for those outside of driving distance of San Francisco for that weekend, has resulted in us not being able to secure San Francisco as a location for WonderCon in 2013.
However, because we knew there was a possibility of not being able to return to San Francisco, we have scheduled WonderCon: Anaheim to be held March 29-31, 2013. Hopefully we will be able to return WonderCon to San Francisco sometime soon.