Just some idle thoughts.
BioFuels may be clean but they are far from friendly to the environment. We already put large pressures on the environment to provided food for the masses. To have a completely BioFuel based economy will expand land usage greatly. Land that is already under pressure may be pushed to far. Farm land needs fertilizers, pesticides and leads to soil degradation and salinity. Great forest are being cut down to produce meat for fast food chains, and now add 5 litters of BioFuel to the trip to get a burger and those forests will be gone before you can blink.
Hydrogen is the best option, but it depends on the energy source. Unlike bio fuels hydrogen can be produced from total renewable sources (Wind, Hydroelectric, tidal, and solar energy). Yet to base your economy on hydrogen generated via renewable sources is still a little impractical. The only option at the moment is Hydrogen produced from nuclear power. I believe that is the way the USA wants to move. And with luck fusion reactors will come online some time this century and with the Hydrogen economy in place, it will become the cleanest economy.
Ethanol based fuels don’t last long. They tend to absorb water from the atmosphere, which can cause damage to current engines. Especially 2 stroke engines. You should not use an Ethanol mixed fuel after its 6months old. I go out of my way to ensure I don’t have an ethanol mixed fuel for my engines (lawn mower, chain saw, edge cutter, whipper snipper, blower vac). I want these machines to last a lifetime.