look at the Suzuki Burgman 400 or Yamaha Morphous 250.
Both are fully automatic transmission, and both have more than enough power to keep up with freeway trafficm although a 250 is the very smallest I'd dare to try an Interstate on...the 400 class will handle those speeds much better.
Licensing depends on your state's laws as to size, etc. I'd recommend having a license, as it can't hurt your insurance rates. Taking and passing a MSF course in a lot of cases will give you a sizable discount. (Note than in some states, passing a
Motorcycle Safety Foundation course grants your license upon completion, or a waiver of the road and written tests.)
The only natural progression is what you are comfortable with yourself. I jumped at 16 from a 90cc Yamaha Enduro to a 650 Triumph and had nary a problem, even with the shifter and brakes being on the "wrong" side from the Yamaha. If you're uncomfortable with the idea of a manual clutch and shifter, nothing's going to allay your dislike of it. The larger scooters will be easier for your wife, as they carry their weight much lower than most motorcycles, so they don't require the physical strength to "prop up" at lights and stop signs if she should find herself a bit off balance.
No more pitfalls on used bikes than on used cars...as always, buyer beware. However, a used scooter is much less likely to be a victim of rider abuse as a motorcycle.
Nothing is going to put your reluctance behind you. But you have possibly more chance of being injured in an accident with a small scooter than a larger one or a motorcycle. Smaller wheels and tires mean road objects and potholes are more of a danger than on something with larger diameter tires. Also, acceleration and braking are susally superior in larger nikes...the chance to *avoid* the accident increases with braking/acceleration/maneuverability.
Motorcycles are not inherently dangerous. They are superior to autos in their ability to avoid accidents...provided the rider is capable of reacting as appropriate to the situation. You also have to ride defensively, and act as if you are invisible to autos. Think ahead, and look down the road.