I'm based in San Francsico and find myself a very happy Continental elite member here. The Presidents Club folks are generally pretty good at helping me find decent seats without that 6'4 350 pound person in the middle seat. If I were you, I'd stick with either OnePass or maybe the AS Mileage Plan as my secondary program. You might want to note that as of recently, and this has not made it to the CO website yet, PC members can visit the SFO AS BR at any time.
Personally, I prefer SFO/OAK-EWR...but if you prefer OAK-JFK B6 just does a better job than UA. In my years flying UA out of SF the preponderance of flights have been late and the service is, I feel, the second worst in the business. (The worst being Ryanair.) Although B6 is an all-coach prouct with a lame ffp, who needs upgrades when you are in a nice and large leather seat with DirecTV and excellent cabin service?