funny, every fuel cell design i can find runs off liquid hydrogen and oxygen, not deconstructed methane.
the energy needed to break methane (or water) into o2 and h2 so it can run through a fuel cell is waste, fuel cells also generate significant heat waste.
fuel cells are great in space, where excess heat is a GOOD thing, and the already exorbitant energy requirements for lifting the needed food water, h2 and o2 for use in other applications, simply makes fuel cells the best choice. IN SPACE.
on earth not so much.
down here, we dont have to fight the gravity well, so hydrocarbons are a good solution for our power needs.
also, protip: fuel cells dont make CO2. they make H2O and massive amounts of heat as their waste product.
http://auto.howstuffworks.com/fuel-efficiency/alternative-fuels/fuel-cell.htm