Mike O knows BART operations like nobody's business. He's walked us through his reasoning on why BART no longer has a transfer connection between the Pittsburg line and the Fremont-Richmond line. It goes like this:
BART, as we know, is old. Though BART has renovated some of its train cars, it's still a challenge to keep barely enough cars in functioning condition. So, the schedules are designed to turn around trains as quickly as possible at the end of the line--otherwise it could take more cars to provide the same level of service, and BART doesn't always have more cars. (Another reason for this is probably to avoid the cost of staffing extra trains.) It's gonna get even trickier when (ahem) the SFO extension opens, because BART will need 39 more cars each day. Okay, so BART had a schedule that allowed transfers at 12th Street and that also had trains turn around asap at the end of the line. But with SFO, there's a new end of the line. And when you make a schedule that quickly turns trains around at the new terminus, then juggle things around so that schedules don't conflict at choke points like the transbay tube, well, it just turns out to be impossible to save the transfer at 12th Street.
Keep in mind, this is only a theory. No one at BART has said this or confirmed it. But, seeing as BART says nothing, this theory is all that we have to go on.