Electricity is the end game. If every car in the US was electric, then the only pollution controls we would need to worry about would be the proper handling of batteries, and how the electricity to power the cars is generated. The battery issues are already accounted for, so that just leaves production of electricity to handle that many cars. Do it via nuclear, solar, and wind combo and you virtually eliminate the carbon footprint. That is the end game.
The greatest risk to algae fuels right now is battery technology and grid capacity. FWIW, a woman discovered a few years ago that she could make a virus replicate itself into a basic battery. The idea is to grow organic batteries that can be tossed in the garden or your garbage disposal without any harmful effects to the environment. Smart woman.