I think you guys are getting distacted. Obivously energy is always conserved. Apart from certain loss processes (drag, friction, etc) energy will always remain within the system.
However, the body is primarily restricted by the power it can deliver, not the energy. It doesn't take any more energy to move an elephant up and down a ladder than it does a paperclip (zero in both cases), but your body will waste a lot of energy in order to muster the necessary power to move the elephant.
Furthermore, it's better to retain control over acceleration/deceleration with your legs. If you invest energy in getting a large wheel up to speed then you risk losing that energy if you need to brake, but if you keep the energy in your muscles then you don't risk as much. On average the higher risk should translate to more energy lost due to braking.