I created several maps for SPUR back in 2008 for their policy paper on regional rail "A Mid-life Crisis for Regional Rail". You can see all the images on my flickr account.
This one shoes short term urban improvements including:
- BART Metro - between Daly City and Downtown Berkeley and Daly City and Coliseum - trains would be more frequent, probably shorter, and look more like subway cars, i.e. fewer seats since they wouldn't travel as far
- Contraflow Lane on Bay Bridge for Transbay Buses
- Add new BART train control to allow more trains per hour to pass through the Transbay Tube and throughout the system.
- Add capacity and increase speeds on the Capital Corridor
- Electrify Caltrain
- Central Subway, including a stop at North Beach
- Caltrain to Transbay Terminal (aka CDX - Caltrain Downtown Extension)
- Upgrading downtown SF BART stations - aka increase station capacity
- New Transbay Tube (with 4 bores)
- Dumbarton Rail
- Vallejo Capital Corridor service crossing at Carquinez Strait
- BART to Livermore
- Extending SMART to San Quentin where a new ferry terminal would be built.
- many others.