Toyota Unveils Plug-in Hybrid Prius
Making hydrogen results in a significant net loss of energy. After you've made it, transporting it is a huge problem because hydrogen likes to leak right through most "solid" materials. It has a very low energy density at one aatmosphere, so it has to be compressed to insane degrees to get any decent portability out of it. Both in tankers and/or pipelines and in the target vehicle. That also means fueling presents some serious issues.
Making hydrogen at STP is about 60% efficient. I've heard 80% claimed for dedicated plants. By comparison, an internal combustion engine is about 30% efficient. I remind you that supercapacitors and batteries aren't lossless either; internal resistance bites you hard at high currents, and equivalent series resistance of supercapacitors, especially, is quite high.
Hydrogen transport does have leakage, but leakage is only a serious problem if you're storing hydrogen for weeks before using it. Especially as you still wouldn't be able to store the equivalent of a full tank of gas with a hydrogen hybrid, you'll lose negligible amounts of hydrogen to diffusion.
Hydrogen does indeed have a storage density problem (it has to be stored as a compressed gas, which means a heavy cylinder for a relatively small amount of hydrogen). Still much better energy density than batteries or capacitors. My money's still on methane or methanol.
Ethanol has already caused corn prices to tweak all kinds of ways; not a good thing. At least at this point, that's a really bad side effect. Corn is a mega-important food crop. Ethanol is like gasoline, in that it must be delivered via tanker, at a hidden energy and pollution cost. It is carbon neutral, in that the carbon in the plant came from the atmosphere, and goes back to the atmosphere as exhaust.
I'm talking about methanol, not ethanol. If methane or methanol are adopted as fuels, they'll be strictly used as energy storage media, formed by burning waste hydrocarbons (chaff and other inedible plant parts) in a hydrogen atmosphere. Closed-loop systems could be built, too, but they tend to be too heavy and bulky to be worth putting into a car (CO2 is scrubbed and bound as a carbonate, then released by heating and reacted with hydrogen during recharge).
This means taking an efficiency hit vs. using hydrogen, but in return you get fuels that are much easier to handle and that can use existing infrastructure (natural gas pipelines for methane, liquid fuel transport network for methanol). You're still way, way ahead of batteries (the reaction that produces methane is quite efficient, and methanol only slightly trickier).
However, electrical vehicles can be 100% carbon negative, as a hydro plant, nuke plant, wind plant, tidal plant, geothermal plant, solar plant... none of them produce carbon at all.
This is still carbon-neutral, as no carbon goes into or out of any part of your system. With ethanol production or synthesized methane or methanol, you grow extra plants that would otherwise not be grown.
The last thing - but not the least - is that to get the most power to the ground, at the least cost, electric wins hands down. Electric motors today are easily manufactured to be lighter and provide better torque and power curves than any internal combustion engine ever made in even a slightly comparable size class.
Fuel cells use the same motors that a battery-powered car uses. The only difference is the delivery system. You could even use a gas turbine instead of a fuel cell, and still come out ahead (this is done for locomotives and ships all the time). In both cases, you don't have to worry about battery lifetime and disposal issues (the catalysts in fuel cells are much less nasty than the materials in most batteries).