TR quotes professor Ernest Moniz, who has a list of shorter-term technologies that deserve more funding, including advanced internal combustion engines and new techniques for burning fossil fuels more cleanly in power plants. Specifically mentioned is the homogeneous charge compression ignition (HCCI), which could run efficiently on a wide range of fuels, with advanced electronic controls.
But the problem is a lot deeper than that - as the article notes, in real dollars, energy research funding is less than it was 20 to 25 years ago. Perhaps that will finally change now that high oil prices have everybody's attention...