On-site generation largely resolves the transportation issues. Your other points are valid, but surmountable. Methanol or Ammonia Reformers and Fuel Cells will be technologies to watch...And once you've got this "renewably-produced" hydrogen (Ha! Look at the >lifecycle< environmental impact of wind and solar), we'll need to compress, transport and store it. Not easy. And you'd best start with clean water--something that isn't in universally abundant supply--good for drinking, producing food, etc.
Most hydrogen produced today is made using natural gas as a base stock--that's a LOT less expensive than electrolysis, and environmentally more sound (considering that electricity--from any source--would be best used to displace electricity produced by dirtier/more expensive sources.)
For fuel cells, expect that the first practical ones in widespread use will use fuels that are liquid at/near typical ambient temperatures--just like our present hydrocarbon transportation fuels. It's an incredibly compact and convenient way to transport energy.