It's a little more difficult to store and transport than methane, yes. If that turns out to be a deal breaker, you can always upgrade the hydrogen to methane using atmospheric CO2. You lose a bit of efficiency, but perhaps that's cheaper than upgrading the storage and transport infrastructure.
These steps reduce the efficiency of the fuel.
Yes, I said that. Efficiency doesn't matter, only cost matters. They correlate, but they're not the same.