They produce a lot of heat, and not enough electricity. Fuel cells are completely silent, and much more of the energy is converted into electricity. Large coal, oil or gas power station. Fuel cells, with their very high efficiency even at low powers, their silent operation, their simplicity and inherent reliability, are the best type of energy converter for CHP systems - the only trouble is that at the moment they still cost more. Another very important boost to fuel cell use has been given by recent decisions of some US state governments.
Rechargeable batteries are very heavy and take a long time to charge.
The fact that fuel cells need hydrogen fuel is a problem for the motorist, as it is not readily available, but this problem is more easily solved for buses, since only one point of supply is needed, the bus garage. The third important area is for mobile equipment . We all like to use mobile phones and portable computers, but for most flexible use we would like very long lasting batteries that can be recharged instantly. The energy density of hydrogen stored in metal hydrides, or in methanol, far exceeds any of the rechargeable battery technologies. This is why there so much research develoment directed at methanol fuel cells.