The ultimate plan is LA->SJ, which is a reasonable compromise and avoids a lot of the reasons why connecting to SF directly via HSR is impractical (it would essentially require a complete reworking of Caltrain to accommodate HSR trains, because there's no alternative anyone would accept to build another parallel rail line up the peninsula).
Not sure what you mean - California HSR trains will go into San Francisco as part of Phase 1 (which is really the second phase, the Initial Operating Segment (IOS) I guess is like Phase 0). They're doing electrification and upgrades of Caltrain there to accommodate it.
