You raise some excellent points, and it will be interesting to see which technology prevails over the coming years. Perhaps both fuel cells and batteries will be popular.
I think along with your big question, is the question of where will we get all of the hydrogen if fuel cell vehicles become popular. Generally it comes from electricity, but in very inefficient means (when compared to the alternative of charging a battery with that energy).
A big inspiration I've had for being pro-BEV (battery electric vehicles) is the guy that runs
this EV webpage. His name is Darell and there's been a huge discussion on a (believe it or not) flashlight forum.
Here is part *10* of the Alternative Fuel Vehicle thread that's been going on for quite a while now. Darell posts regularly, and really knows his stuff. Of course, he is a bit biased since he owns an EV, and used to lease another one. He has solar panels up on his roof...check out
this video on how he recharges his EV. If only we could all recharge our cars for the equivalent of $0.90/gallon in our own homes.