You have been assigned to a scientific commission whose mandate is to research ways of reducing air pollution from motor vehicles. Your specific assignment is to research the types of alternative-fuel vehicles that are currently under development, examine the advantages and disadvantages of each, and decide which would have the least environmental impact.
* Natural gas
* Fuel Cell
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OK, you list four technologies....and some overlap and a couple are not listed at all. So I will entertain these and a couple more. However, first and foremost let us entertain the underlying premise. That is the personal motor vehicle. It seems that this "commission" accepts the premise that in order to solve this energy issue it is needful to support the motor vehicle and not to address the overarching issue of public versus personal transportation within the context of urban design. So be it, but you might entertain the idea in theory at least, that a true solution to these issues would be to alter the urban paradigm to not be as needful of personal motor vehicles within the urban border. A city designed without them would be more spacious in many ways, certainly less "jammed", and definitely cleaner. Think about it.
However, even if this were addressed, one would need; A) the motors for mass transit systems, and B) the motors for transport connecting urban zones (and rural folks to the rest of the world). So even if we take the majority of personal motor vehicles out of the equation, we are left with "some." However, under the "new urban design" scenario, the large majority of transportation could be shifted to "track-based" (light surface rail, Segways, bikes, air- or electric carts for short distance...subways, elevated trains for longer shots and for transport of goods.) Thus electricity could be tilted to serving a much larger population. However, this would leave open the question, could we make enough electricity. I should think the energy saved from personal vehicles would be more than enough.
As to the rest of folks that do need personal motor vehicles, and/or the scenario that presumes their needfulness, let us address the various technologies. First amongst these, we will posit that the idea of "hybrids", meaning a technology that captures otherwise wasted kinetic or potential energy, significantly improves energy efficiency and should become the "status quo" in any case - bar none. (And contrary to what the big automakers would have you think, hybrid technology has been known since the late 1970s / early 1980s. Only now have they bought into the idea however.) The current hybrid technology can easily achieve 70+mpg [see: http://www.hybrid-vehicles.net/DaimlerChrysler-ESX3-hybrid.htm ...
Overview of alternative fuel vehicle technologies and rationale for selecting one to promote.