Then again, some legs on the PHL-IAH-SMF flight are upgraded even for Silvers, are usually much cheaper than the EWR-SFO direct, and faster in terms of check-in and baggage.

SMF is an hour and a half from SF. Considering you will have your rental car within minutes (and at half the cost of SFO), it is a viable alternative. If you are flying into SF to do wine country, it is actually your best bet.