First of all, the density of hydrogen is very low. Even if the fuel is stored in liquid form in cryogenic bottles or compressed gas cylinders, the energy stored in those spaces is very limited, and hydrogen vehicles are also very limited compared with other vehicles. Some studies have used special crystals to store hydrogen in a higher density environment, and it is safer.
Another method is to extract hydrogen from traditional fuels such as methane, gasoline and ethanol without storing hydrogen molecules. Many environmentalists are not interested in this idea because it depends on fossil fuels. However, this is an effective reorganization procedure. Using recombinant gasoline or ethanol to drive fuel cells is still more effective than using internal combustion engines.
Secondly, it is very expensive to manufacture reliable fuel cells to provide electricity for hydrogen-fueled vehicles. Scientists are working hard to study the basic problem of making fuel cells as cheap as possible and hard enough to withstand the impact and vibration of cars. Most fuel cells are fragile in design, so they can't be preserved under that condition. In addition, many designs need rare materials such as platinum as accelerators to make the work more smooth. Accelerators may pollute the purity of hydrogen and adversely affect the supply of hydrogen.
The third problem is that hydrogen can be used as a carrier of energy instead of energy. It must be extracted from fossil fuels or other energy sources, thus causing energy loss (because the conversion from other energy sources to hydrogen and back to energy is not 100% effective). Because any energy source has disadvantages, switching to hydrogen will lead to a political decision on how to generate this energy source.
Recently, a method has successfully produced hydrogen directly from the sun and water through a metal catalyst. This may make it a cheap, direct and clean method to convert solar energy into hydrogen.