I'm not sure what annoys me more, that BART doesn't go to Emeryville or that Amtrak doesn't stop at a BART station closer to San Francisco. In reading a Contra Costa Times article, the main person in the story commutes via Amtrak from Martinez. Martinez downtown is very isolated from other transit options in the region including BART, yet it is the county seat with all the government office buildings and courts where people have to go for jury duty. It's also a nice transit oriented downtown when it comes to its proximity to Amtrak. This is good for a San Francisco connection, but not Contra Costa County (That's a whole other discussion).
However Amtrak makes you get off at Richmond if you want to BART into the city. There is also a bus from the Emeryville Station but that isn't so direct and could be eliminated with better service. What would be nice to see is a direct link from Amtrak to the West Oakland Station or BART extension to Emeryville. Emeryville is emerging as a dense city willing to go up because it has no other choice. It also attracts lots of retail and major employers because of its inexpensive tax burden compared to Oakland or Berkeley. This is a no brainer connection that would increase BART's reach while also increasing Amtrak's reach. You can see the current transfer and how indirect it is removed Emeryville is below.
I think a more comprehensive metro system would be better to connect all the places but the MTC and others haven't been talking a lot about real core capacity increases like they should. The easiest would be to build a small loop track for Amtrak next to the West Oakland BART station. There's room and you could even use the aerial rights to pay for the small improvement and transfer station. This would pay off huge. West Oakland is the best connected station in the East Bay with more trains coming through than any other station. With the Amtrak Connection, you could get from Sacramento directly downtown without much waiting, considering the 2 minute headways into San Francisco at West Oakland in the mornings. Also, its a faster way to Oakland than from the Richmond Transfer, which is good if you're going to Berkeley. This would be a very cost effective option in my opinion to make Amtrak more attractive and might even create the need for even better service.