One of many beyond the end of the double track main. [www.google.com] Looks rural, but there are hourly trains each way off-peak, rising to 4 or more an hour peak direction. With grade crossings. On single track with 3rd rail and occasional sidings (some for passing, some mainly drill tracks for freight). With (IIRC from my one trip out there) 4-6 car trains even off-peak. Here's another one, just west of the Ronkonkoma station, which is the end of the line for electric service into NY (diesels continue out to the Hamptons) [www.google.com].

Caltrain also has many grade crossings, with high train volumes during peak periods moving at up to 70mph between stations that are fairly close together. Yes, they'd like to get rid of them, but the money isn't there to do it everywhere and/or quickly unless HSR kicks in, electrification or not. In terms of passenger and train volume, and train length, it's not even remotely comparable to SMART.

SMART is a commuter train that, even at peak periods, might run as many as 4-6 trains in a peak hour, counting both directions. Probably less, until the ferry connection improves. Yes, there will be some privileged Marinites who are delayed by a minute or 2, and yes, San Rafael is mad because they expected to have another 10 years to pump up the opposition before being required to deal with the Larkspur extension (which will cost much less for being done sooner - inflation y'know). They agreed to the arrangements, and would be dumb if they did so without some preliminary plans for the transit center changes in hand, and now it's going to cost them some money. It's Marin: the people have money, they just don't want to spend it on stuff like a transit center that most of them won't ever use (being wedded to their cars). Nobody was ever going to build a structure across downtown SR (either one of them) for the low train volume expected on SMART.