The objective issue is that scooters have automatic transmissions, which make them quite a lot easier for many people to handle. Subjectively, they are in general much less intimidating, which seems to be a positive for the scooter crowd and a negative for the motorcycle crowd.
But I think the automatic transmission is the big thing. Honda tried to sell auto transmission motorcycles a while back, but nobody wanted them.
Honda's selling new CVT-based automatics now, the spacey DN-01 and overkill-redesigned VFR1200. Very expensive and aimed at no discernable market (unlike the old Hondamatics you mentioned). I haven't seen a single one on the road yet.