Plant based biofuels are only problematic if you imagine replacing all transportation energy needs with them. Cut that out! Develop all technologies and let the market decide. I predict that there will be specialist niche applications for biofuels, and that most of transportation will be electric. For a cheap, robust means of storing lots of energy, it's really hard to compete with a metal tank of hydrocarbon fuel, but this doesn't doom us to run everything this way.