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.
2002 Vulcan 750, 2013 Royal Enfield B5
2001 XT225, 2009 Genuine Stella
2012 Zuma 125, 1980 Puch moped