Electric bicycles are actually more efficient than bicycles (which are themselves more efficient than walking). The combination of human power and electric assist uses less total energy than human power alone!
I'd imagine the movement of the legs while pedalling would affect the aerodynamics, but is there something else happening?
More complex braking system might introduce a lot of problems to a bike where that should be a simple thing, probably easier to have extra set of hydraulic brakes in case the battery is dead.
Keep going this way and you'll eventually reach the efficiency of converting solar power to movement, which is again directly comparable, and electrical systems win compared to biological systems.