Hydraulic flaps need a mechanical connection or they will not extend or retract equally.
Extending or retracting equally is not as important as you imagine. As long as the system is not binding somewhere more on one flap than the other, the air loads will balance the flap position in flight. You'll never be aware that there was a difference. Full down flap would be even. Full up flap would be even unless there is a mechanical restriction (tight hinges maybe or whatever else prevents Cub flaps from fully retracting?) preventing the flap from going full up. To be certified without any mechanical connection you will have to demonstrate full aileron control with one flap down and the other locked up in a crosswind. If it is not controllable in this condition you will need either a flap indicator on each flap or the two flaps must be bused together mechanically. That could be as simple as just one balance cable between the bellcranks in each wing.
A flap hydraulic system could power the flaps in both directions or just down with a spring used for up. With a spring return you would only require one hydraulic line where the other would require two.
Another option which would take up more space due to the large size of the actuator, would be pneumatic vacuum. The Stinson V-77 and Waco VMF-7F had vacuum systems. You could leave the control valve on the Stinson down all the time, not that you'd want to. The air loads would control the flap position. On a go around they would automatically retract. These systems were difficult to modulate to an intermediate setting.
On a Super Cub you could attach one actuator behind the baggage compartment to the existing flap cable. This actuator should have a return spring, either internal or external only for the purpose of returning the piston to the flap up position. One hydraulic line to the actuator pump with a lever/button actuated spring loaded check valve mounted wherever you want it between the pump and actuator. To operate, just pump a handle the desired amount for the down flap. To retract just push the lever on the spring loaded check valve for the desired amount of retract. If the flaps retract faster than desired, a restrictor (full flow in one direction, restricted in the other) check valve can be inserted in the hydraulic line.
Make the area of the actuating piston large enough to provide the force against the full air pressure against the flaps. The pump would have a much smaller area so that the pumping forces are low enough for comfort and finite flap position adjustment. You could jury rig a spring scale to the existing flap cable in order to determine the required force. Then it would just involve a few simple calculations to determine size of components only if you wish to get fussy with your design. Make sure that the actuator has enough travel for full flap operation. Rather more than not enough would be preferred.
Rather simple once you put your mind to it. Just a bit of labor to make it happen. Oli is a clever guy, I'll bet that he could make the entire system in his shop without a great deal of expense.