I think all of the major cities should switch their trains and buses to Fuel Cell vehicles. Fuel cells already work and are viable in larger vehicles (although not cheap). However, one of the biggest issues with large cities is air quality. The government should not be another contributor.
No public transportation should be emitting these pollutants. This comes with the benefit that since major cities will be using hydrogen on a larger scale, there will have to be refueling stations in the cities. The refueling stations will provide a place for consumer purchased fuel cell vehicles to fill up.
I also think the new vehicles should not be fuel cell only. We know that hybrids reduce the amount of fuel that is used, that should not change with fuel cells. The hydrogen may be cleaner and not produce pollutants, but it will still need to be filled up. Using hybrid technology that is already being used should be able to be used in conjunction with the fuel cells to make the vehicles travel farther on the same amount of hydrogen. This will also help to alleviate the amount of hydrogen that needs to be produced to fuel the public transportation system.
Once the large cities have it working, the medium sized cities could then also get on board.
C'mon government. You want to say you are building an energy driven economy and fighting global warming at the same time. Stop taking useless 3 or 5 mpg increases over 10 years, and jump into removing all gasoline use from public transportation. Get the buses, public, then school switched over. Then mandate Tractor Trailers switch and get the biggest fuel hogs immediately off of gasoline. The smaller vehicles will continue to get more efficient, or will make the jump to fuel cells. Make that happen!