Third rail, like that used by BART, has a large number of disadvantages and is generally only used for urban subways. The main disadvantage is the huge safety problem: while overhead electric wires are safety out of harm’s way, a 600 to 1000 volt energized rail at ground level is a major safety hazard. This means that a system using third rail must be completely separated from the possibility of human contact, which means many hundreds of millions of dollars of cost to completely fence off the line and to remove all road crossings immediately. By contrast, grade separations are not mandatory with overhead wires.
Another disadvantage is that third rail systems can only provide a limited amount of power. Propelling trains at high speed requires a lot of power, and the higher voltages carried by overhead lines make it easier to provide faster Caltrain and future high speed rail service. Overhead wire is that choice for all new railroad electrification projects around the world, with the exception of some subway systems.