In my opinion it is all down to what the manufacturer meant for the bike.
Very high HP per liter engines usually waste fuel.
Recipe is simple : long duration camshaft with a lot of overlap, very short stroke for a lot of RPM, short inlet track for high RPM max power.
But the recipe for high FE is pretty much the other way around ...
Except for the general freer breathing
Then it's a matter of vehicle efficiency :
sports bike offer longer gearbox ratios and refined aero, top notch accoustic tuning of exhausts and inlets, state of the art injection and other fancy equipements.
My conclusion is, for a given capacity, less cylinders is usually better if you want to stick to sensible speeds.
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