I am not that experienced with float planes, but I did try my Sea Fazer with flaperons. It leaped off the water and pitched up. It was not a good take off. It is a .46 powered fun fly plane so it has more than enough power and this may have contributed to the pitch problem. All the rest of the sea planes I have flown have been normal configuration and have had no problem.

I would think your Cub will have plenty of lift to get airborne so rather than complicate the plane, I would fly it as is.