My scheme was similar to yours, but with lighter construction since the long bridge from the existing railroad r/w would only hold a (preferably covered) walkway with moving sidewalks similar to airport concourses.

SMART's preferred alternative back when they did the DEIR in 2004 for the whole system (before money problems cut the first phase back to San Rafael-Sonoma Co. Airport) was a direct rail connection on structure to the ferry terminal, or at least to the shopping center across the street. See: [www.sctainfo.org], scroll down to the Draft EIR section (or just go to the end of the page), and look at the station summaries appendix ( [www.sctainfo.org] - large PDF file). Go to page 52 or search for "Larkspur" in your PDF reader. Given that cost went up and funding didn't, they had to drop the Larkspur-San Rafael segment for initial construction, as reflected in the Final EIRs.

Be aware that the "mouse" has a real bug regarding BART - evil conspiracy etc. While nothing is truly impossible, I don't see BART doing anything related to Marin within most of our lifetimes if ever - the money isn't there, the traffic isn't there, SF would have a cow regarding a Geary Street BART line, the GGB is still not really BART-ready, and the tunneling project just to get it to Marin City after you get off the bridge would be massive. Just.Not.Going.To.Happen. SMART is a North Bay line, and any connections to SF will be via GGT ferries and/or buses. And yes, electrifying it would be a Good Thing especially from air quality and GHG perspectives, but the traffic just isn't there to justify it right now.

Welcome to the ongoing saga (sometime factual, sometimes imaginative) of SMART at Altamont!