What about casting the flywheels out of lead?I think you're right that it's not going to scale well. The first and primary issue is that the "size" of the engine is related to it's linear dimensions, while the mass is related to the cube of any given dimension. So the mass does not scale linearly with the size. I'd wager that this is the biggest hurdle.
I'd imagine that this could be "somewhat", and "to some degree" be addressed by carefully selected materials to get the reciprocating parts as light as possible, and (maybe.... Thinking on this...) to move the concentration of mass in the flywheel as close to the circumference as possible. Not sure on that one yet, that's math I haven't done since I don't remember when... Still, it's probably going to be difficult (at best) to overcome the weight to size ratio.
Or lead weights installed in them.