Per wikipedia, a thermoelectric generator has typical efficiency around 5-10%. Not worth bothering with imo - using the motor as a generator should be 60-80% efficient, depending on how well the batteries accept high charge rates.
Energy recovering shocks would be quite cool. I bet these are still in the prototype stage, and they sound like they work best for heavy vehicles - the mit article discusses using them for large trucks, military vehicles, 18 wheelers.
The Empulse is perhaps the most refined and productized of the near-term electric bikes available in the short term, but still has a great deal of room for improved efficiencies. Think of a 50 mpg 1984 Honda CRX HF vs a 50 mpg 2010 Toyota Prius. Brammo is basically releasing the EV bike version of the CRX - a solid bike using advanced components, but without significantly advanced control systems ($$$ to develop and get "right", see Richard230's GPR-S). Those control systems will come with time and increasing market, and I would not be surprised to see advanced control systems be a significant discriminator between the smaller manufacturers (Brammo) and the big motorcycle companies (Honda..).