Geometry
The biggest difference is the frame geometry. As you probably now know the Townie's *flat foot* technology places the seat back from the pedals much further, and slightly lower than normal geometry.
As others have noted most of the big manufacturers have started building *crank forward* or *flat foot* geometry bicycles such as the Trek Pure. They also build bikes with geometry designed to move the majority of your weight to your bum (not your hands) with traditional crank placement such as the Trek Navigator's. The standard answer is to test ride them and see what fits and feels the best.
My wife had a really nice Trek 7.3fx (wish we hadn't sold it, our daughter would fit it now). She is a little overweight, and the added stress on her hands caused a lot of numbness and pain.
We finally purchased her the 21spd 700c townie, and she loves it. I accidentally *cough* upgraded the wheels to ultegra/Mavic CXP33's (why we went 700c), changed the shifting out to a 9x3 SRAM x.7,x.9 mix, and put on some 700x32 kevlar beaded/belted Panracer's. It is now much faster than it looks. We later added a rack, fenders, and wicker basket to use it for the usual evening family rides or light touring on rail trails.
I have a Jamis aluminum/carbon road bike and a trek hybrid. After riding her Townie doing maintenance I broke down and purchased a Sun *Ruskin Sport* that has very similar geometry to the Townies (more modern styling) and 700c wheels for $330 ($400 now?). The components are pretty low level as the price suggests, but have already started replacing them anyway. The first to go was the terrible seat and post, replaced by the very nontraditional *Spongy Wonder* seat atop a decent quality aluminum post. The seat works with the geometry really well, it feels like your simply leaning against something while riding. Replaced the wheels this week with some decent road wheels, and will replace the drivetrain soon.
If you are wealthy the Ran's Crank Forward's (they claim to have started the trend) are probably the best built and use the best components, but they come with the price tag to match.
Good Luck, and let us know what you bought, and how it is working!