Certainly there's a trade-off between the inefficiency and weight of an added converter, and the efficiency of the motor over a wide voltage range. If you can find a motor that will drive the vehicle over a wide voltage range with reasonable efficiency, then that would be preferable.
Since the 5F, 5V cap stores twice as much energy as the 10F, 2.5V cap, the 5F is the preferred choice for maximum energy storage. But if the motor maximum is 3V then you may need some sort of voltage converter or limiter for that. That is best determined by testing of the motor with the capacitors.
For charging the caps, a power supply set at the cap voltage with a current limit should give you a fastest charge.