The difference in acceleration between the smaller engine and the bigger engine is probably trivial. They would both be blindingly fast compared to a car. Even if pulsing 0-60, the difference is a few seconds. You'd probably use more gas with the bigger engine to do so.
Disregarding pulsing and gliding, I can address this issue from personal experience from the standpoint of sportbikes - motorcycles designed to go fast around a track, NOT get good fuel economy. I've owned a Ninja 300 and a CBR 600 F4i in the last year. The Ninja 300 was ALWAYS more efficient than the 600. The 300 is more efficient than the 600 at any speed you think you could get away with on public roads. You could try to ride your 300 at 100 MPH till the tank runs out and compare that with the 600 and you would never get better mileage on the 600. The 300 would typically give me mid 50s to mid 60s MPG. Could go about 230 on a tank before thinking about refueling. The 600 typically gives me mid 30s to low 40s and my low fuel light is on by 130. The 600 is designed to be stupid fast and is a comparative pig in regard to fuel consumption and emissions. Motorcycles in general are incredibly inefficient and incredibly polluting compared to cars due to lax emissions standards on motorcycles.
If you compare apples to oranges, a touring bike, which actually takes fuel economy into consideration, would come closer, but the smaller engine should still consistently beat it. Your best bet would be to start with something small that is available in abundance such as Ninja 250, Ninja 300, CBR 300 or 500, or whatever else you can find in your area. These vehicles are incredibly efficient as is. You could make efficiency gains with extensive aero mods if legal in your area.
If you don't want my personal opinion, DON'T read the following!
If you are going to ride a motorcycle, don't mess with pulsing and gliding! From a pollution standpoint, you're doing way more damage no matter what compared to driving a car. From a fuel economy standpoint, you're already getting way better mileage than most cars--with sporting performance factored in, there is NO comparison. From a safety standpoint, you're making an unstable vehicle even more unstable and putting yourself at greater risk from other vehicles. Ride for the thrill and try to keep the rubber side down.