In any kind of full-wave rectifier off a generator, you will only be using a portion of the WAVEFORM, however you will not be wasting significant energy as if you load the generator more, it will require greater input energy to turn. During the period in which your circuit is not conducting, the generator has no effective load. The only loss is friction and perhaps some parasitic magnetic effects / eddy currents etc.
If the energy required to turn it is negligible, you might want to consider a way to harvest the energy - perhaps some kind of psuedo active-PFC circuit, which would utilise more of the waveform, although with a low input voltage, the advantages are going to be fairly minimal.