One disadvantage is the arable acreage that is required to grow enough biomass to provide enough energy to satisfy demand. In Brazil, significant strides have been made to use this type of fuel to replace gasoline, but they have the luxury of much land, a long growing season and a smaller population to provide with this transportation fuel. The United States does not have that much additional farmland to provide for its significant demand, which means that acreage that is devoted to providing food crops would have to be diverted to energy production.
Another disadvantage is that burning the fuel still releases carbon, so the pollution problems presented by fossil fuels are not fully addressed with the use of biomass.
Hydrogen is cited as a relatively safe, clean replacement for organic (carbon based) motor fuels. It may be burned as in internal combustion or turbine engines, or it may be used in fuel cell stacks to generate electricity for small-scale applications. In either case, the byproduct of the process, or its "exhaust" product, is plain water.