Well this thread is great, I love a good debate, Ive had a change of mind, I think Rizzo is right though.
The piston can both make and absorb energy, the flywheel weight will only vary the rate at which the rpm increases or decreases. So if you had two idecntical bikes but with different weight flywheels traveling in say 2nd gear at 4000rpm and both rolled the throttle off the heavier flywheel bike's piston will have to absorb the energy of the extra weight, where as the other bike will have less flywheel inertia (energy) to absorb therefore braking will be more effective. Im not talking a huge difference between the two, almost un-noticable.
Newtons Law comes into play here, An object at rest will remain at rest unless acted upon by another force just as a object in motion will remain in motion unless acted upon by an opposing force.
The object being in this case the flywheel, if it is heavier it will have more inertia than the lighter one and will require a larger opposing a force to slow it down. A piston will only absorb so much energy at a time, so a certain amount of absorption will be used to slow the flywheel down leaving less energy absorption to slow the bike down.
Trucks use the same principle, the exhaust brake shuts a flap in the exhaust so that the piston can absorb more energy. It basically turns the engine into a compressor. The act of compressing the air in the chamber is where the braking effect takes place.