I just got my first scooter (Super 8 150). I've owned many motorcycles. Overall I prefer motorcycles but for running around town a scooter makes more sense and is more fun. As for Automatic Vs manual Transmission. Take two identical vehicles (scooter, motorcycle, car or truck), one maual and one auto, and the manual will outperform the auto almost every time- better acceleration, fuel mileage, and better control of the vehicle. This is especially true if the vehicle has a small high reving engine. In case of a very high performance vehicle, it may take a skilled operator to get the extra performance out of a manual.
One more thing, here in the US, there is a very limited selection of small displacement motorcycles, even 500cc is usually considered a beginners bike. I have owned motorcycles up to 1200cc. Overall, I think small bikes are more fun. There is a much better selection of small scooters available here than small motorcycles.