For the cons, well there isn’t much for the only problem they have seen so far is that there was a higher emission level for carbon monoxide (which is deadly to humans) and that it will decrease the engines maximum output to some extent. There is also a nasty trait of BioDiesel that it is a very good solvent that any deposits in the engine or fuel system can get dislodged by the fuel causing clogging in filters, pumps and other fuel delivery parts. After switching to BioDiesel or the other available blends (pure biodiesel or B100 or mixed with petroleum diesel and sold as B20) it is recommended that you get the fuel pump changed and all other parts that are made of rubber in it’s many forms and shapes with non-rubber ones to avoid leaks and spraying you with the stuff.
No fuel alternative is perfect for most of them are still in the development stage. Opposed to the almost century old history of the current diesel and gas powered engines, the technologies for alternative energy/fuel are still in their infancy. There are some who argue that shifting to BioDiesel will increase emissions rather than decrease it. It would also create problems with grain exports for farmers would opt to farm higher yield BioDiesel producing crops than export grains. The landscape would change from diverse fields of several diverse grains to corn or other more productive oil producing crops. An answer to this would be research into using algae (microscopic plants) for BioDiesel production to minimize the economic impact crop shifts would have.
We will surely see more and more green vehicles and alternatives at the gas pump in the future for we have no choice. We have poisoned the earth for so long that the effects are now causing catastrophic changes to our weather and health. We just hope these technologies would filter down faster to the end-user (which is you and me) as they get to perfect their respective technologies before it is too late for mother earth.