Emeryville to SFO

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Richond Amtrak/BART is in a pretty dodgy area. While maybe not a big issue if the Zephyr is on time and it is daylight, I'm not sure I would want to make that transfer from a late Zephyr at night with luggage.  If you are ticketed through Emeryville with the bus to SFF, you can still get off at Richmond and do the direct BART transfer if the timing is OK. If a passengers is ticketed only to Richmond, the Emeryville and bus option is not available.  I would book through to EMY/SFF, then assess my options as the train was approaching Richmond.
 
Wayfinding would be easier at the Richmond station, since it's all one complex. That said, I'd personally cross the bridge on the Thruway bus then either BART or take an Uber/Lyft/taxi from there. From the Financial Center stop, simply walk south (backwards from the bus from the looks of it) past the Hyatt and the cable car stop, then take a right onto Market. The Embarcadero stop, including an elevator down, should be available on the block in front of you, to the left of the Wells Fargo building.

The advantage of this, beyond a cheaper BART fare, is that you're starting on the SFO side of the bay. That means that if the train is significantly late and BART is closed for the evening, you're still able to easily get an Uber/Lyft/taxi without having to pay the higher amount + toll for the bay crossing.
 
Richond Amtrak/BART is in a pretty dodgy area. While maybe not a big issue if the Zephyr is on time and it is daylight, I'm not sure I would want to make that transfer from a late Zephyr at night with luggage.
I've never had a problem inside the station. YMMV.
 
 
Daly City is not SFO.
 
Ah I was just thinking San Francisco and not the airport. Sorry.

I think the BART transfer is still most convenient involving least amount of walking when compared to the other alternatives.
 
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According to the BART Map, the Red Line is still there but it doesn't go to SFO (according to the map).  It gets close to SFO, but only the Yellow Line goes right to SFO.  But all I know about BART is what's on that map.  Maybe the map's wrong or maybe I don't know how to read it.
It's changed over the years.  There used to be a direct Richmond-SFO line, but that discontinued at later evening (maybe 7 PM) where the Pittsburg/Bay Point line went to the airport and Millbrae in some sort of weird loop.  I think at one time the only train that went to SFO was the one from the Dublin/Pleasanton station.  They tried a lot of different combinations over the years
 
I've never had a problem inside the station. YMMV.
The only problem I had was when my kid needed to use the restroom and it seemed locked for 20 minutes.  Not quite sure what was up with that, but when I've been in there I've seen stuff like discarded, ratty clothes.  But transferring from Amtrak to BART or vice versa was painless and easy since it doesn't mean leaving the station.

One time I did actually park at the Amtrak parking lot, which is limited.  Now that was a little bit on the adventurous side.  I went to the McDonald's a couple of blocks away and I had a sense that I had to get out of there ASAP.  I grew up in the area and it was always a downtown area with some unsavory elements, but it felt far different back in the 1970s.  Supposedly the decline was due to major businesses leaving after the opening of Hilltop Mall.
 
Wayfinding would be easier at the Richmond station, since it's all one complex. That said, I'd personally cross the bridge on the Thruway bus then either BART or take an Uber/Lyft/taxi from there. From the Financial Center stop, simply walk south (backwards from the bus from the looks of it) past the Hyatt and the cable car stop, then take a right onto Market. The Embarcadero stop, including an elevator down, should be available on the block in front of you, to the left of the Wells Fargo building.

The advantage of this, beyond a cheaper BART fare, is that you're starting on the SFO side of the bay. That means that if the train is significantly late and BART is closed for the evening, you're still able to easily get an Uber/Lyft/taxi without having to pay the higher amount + toll for the bay crossing.
There is an entrance to BART Embarcadero Station at Drumm and Market next to the Hyatt and cable car stop. No need cross Drumm and wall up Market.
 
If the objective is just getting to SFO, connecting to BART at Richmond is the least-hassle method. Rail all the way, no bus rides in commute traffic, no wandering around looking for a connection. Not the most scenic, but it's simple and seamless. FWIW, I'm writing this while travelling on BART - no complaints.
I live in Emeryville. If your intent is to go to a hotel at SFO airport, I agree. Get off Amtrak at Richmond and get on BART. On BART you will need to change at MacArthur. Simply get off and walk across the platform. This will be much easier than taking the Amtrak bus from Emeryville into downtown San Francisco, then walking several blocks to BART. 
 
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