The reason is simple: Honda designed the entire Integrated Motor Assist hybrid drivetrain for the 2006 Civic Hybrid literally from scratch.

Note that the new 1.3-liter gasoline engine with its three-stage SOHC i-VTEC operation was designed to specifically match the electric motor assistance used in IMA. This is not like the current Civic Hybrid, which essentially uses the 85 bhp 1.3-liter i-DSI engine from the Honda Fit/Jazz integrated with an electric motor assist--not exactly the most efficient combination!

In my humble opinion, we may see EPA ratings in the low 50's for both city/highway driving with the CVT and (hopefully!) 6MT configurations.

DakarM, having driven from Los Angeles to Las Vegas, NV myself there are two significant (and quite steep!) passes you have on Interstate 15 between these two cities: Cajon Pass just north of San Bernadino, CA and the mountain pass south of Wheaton Spring, CA fairly close to the California-Nevada border. ziggy23 probably gained a lot of fuel mileage from going downhill at both passes, which explains why ziggy23 was able to get around 50 mpg on the Los Angeles-Las Vegas round trip. By the way, given the informative display on the Prius, you actually have a visual incentive to drive the car with a feather foot to improve gas mileage.