I have a Genuine Stella, which is a 150cc scooter with a manual transmission. Unfortunately it is not modern, it is an Indian made copy of a vintage Vespa. It looks great, and is a blast to ride around locally on, but not reliable enough for long distance travel, which is to bad, since it's manual transmission would be great for climbing mountains. I have wanted a modern, reliable scooter with a manual transmission for a long time. I don't see there being a big market for such a bike, but it seems there would be a big enough market for one or two manufacturers to sell them. IMO, the Zuma 125 would be great with a 150cc engine and a manual transmission.
Small motorcycles have their place. I would love to have a 250cc cruiser with tubeless tires. I can't handle the riding position of a sport bike. So far the best I've been able to do is an XT225 with a centerstand. At least I have a way to fix those tube type tires out on the road or trail.