BMW 650 are one of the best larger bikes for fuel economy. All the variouse sytems are designed from scratch to be good on fuel. Taking a Ninja 650 and reducing the rpm will work up to a point. as you reduce the rpm you eventualy run into fuel metering problems as well as drivability problems in top gear. You end up having to shift gears more often than when the bike is in or close to as built.
The way I think about engine size and fuel economy is in lbs of air the engine pumps per mile. So that if an engine twice as big turns at half the rpm they consume the same amount of fuel and air. The slower running engine will last longe all else being equil.
I have commuted 84km/day [52 miles/day] on my KLR 650 and it was more than enough for the task. If you later deside you want to stream line it, it will be less hassle than a multicylinder engine. If you can get a fuel injected singe cylinder motorcycle that would be even better for later modification. I think the ninja 650 is fuel injected so it may be better able to deal with changing final drive ratios than a carbed engine, and also better able to be streamlines later on.
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