[Al Skierkiewicz]

Jose,
Each motor is designed for a specific current based on the strength of the magnet. Automatically dumping in twice the rated current may get you nothing more than additional heat. If your motor was rated for 3-6 volts then you are going to see an increase in power with twice the input. All things being equal, power in equals the square of the current times the load resistance. Since you are doubling the current, the power would go up by a factor of four less the losses.
Based on the fuel cell providing one volt, you can use a voltage boost convertor to charge the caps. The charge voltage curve is the inverse of the discharge curve, but remember that at the start of charge, the cap is taking a lot of current. You could then use a timer to place the cap in series with the fuel cell so you get that extra boost (cap voltage plus fuel cell) to start and then switch to fuel cell alone for the remaining time. I bet that if you looked at the 555 timer circuits and you used the capacitor bank as the timing component you could simplify design somewhat.
You say the rules allow charging before the run? Is so, I think you may be able to get the caps charged up. I was thinking, can you also use mechanical storage? i.e. use a motor to run up a flywheel and let the stored energy in the flywheel drive the base.