You're stuck in the "long trip" "it's like a train" framework.
It is neither.
In peak hour it would probably be fine, when everyone is fairly sensible and not drunk. But after hours, I've had quite a few uncomfortable bus rides due to the various anti-social behaviours of fellow passengers. That was with the hand-brake of a driver who obviously isn't getting involved, but can avoid escalating behaviour by stopping the bus or calling authorities.
I have great faith in the technology! I just wish I had as much faith in the people riding inside it :)
Schedule: http://www.mta.info/nyct/bus/schedule/xpress/x001cur.pdf
Also, with a 35-minute trip time, these concerns are well within the realm of "hold it" till the next stop.
Seriously? It's like laying in a not quite horizontal bed for 30 minutes. If you can't plan your bathroom usage 30 minutes ahead of time, then don't use this transportation system (or wear a diaper). I can almost always hold it for 30 minutes after I am really feeling the urge to go. With 12-14 million trips per year, will there be accidents? Certainly. So that capsule gets diverted to be cleaned. Big deal.
> At least on BART you can move away from the crazy
It looks like those spaces are small enough that only 1 person could easily interact with you. If that's a problem, they could probably build in plastic dividers. Or you could just buy two tickets. If you can't tolerate that level of risk, then again, don't ride this thing.
I can assure you that there are plenty of people who are not bothered by these issues.