Have you looked for hotels out of Downtown but near a BART station? BART covers pretty far, if you don't mind a long ride you can stay in Dublin/Pleasanton or Richmond or Union City or Fremont or SFO. The transit system in CA can rival that of the Northeast, IMO. No 24/7 subway service, but a much better bus network.
That's what I did when I went to DC, found a pretty good priced hotel by the Dunn Loring WMATA station.
BART seems pretty expensive and does not offer passes (that I can see). From Union City to Embarcardero would cost us around $28 round trip. It also means not going to the hotel except for overnight. I think I would rather have that cost in the price of a more convenient hotel.