I am one of the few remaining Seattle-area natives. I also get down to the Bay Area frequently on business. In terms of cycling amenities, and perhaps most importantly, the cycling weather, the Bay Area is superior. There are about five months out of the year in Seattle that are relatively rain-free (May-September). The cultural aspects of the Bay Area are better than Seattle. Unfortunately, the cost of living and housing is far greater in the Bay Area, but that can be countered by a better employment picture depending upon your profession.
On the upside in Seattle, is I can be hiking or snowshoeing (in the Stevens Pass area) 50 miles from my house. But unless you already have a job, or have a job that is in demand in this area, prepare for a hunt. You may want to look on the online classifieds in the Seattle and San Francisco newspapers to check out the job prospects.