I don't think this has to do with cams or intake stuff. VVT-i doesn't have separate lobes, all it does is does is alter cam timing.
Looking at the 1NZ-FXE bsfc chart (from a 2nd gen Prius, I know it was updated for the Prius C but it should be similar), the engine probably runs more efficiently at the higher rpm. The lowest fuel consumption per amount of power developed is from 2500-3500 rpm. However, that higher rpm almost directly correlates to more power use. So, we can fairly safely say that going from 1100 to 2200 rpm really means you're using close to twice the horsepower to push your car down the road. This could be due to the higher speed, temperature, wind, inclines, road conditions, accessory use, etc.
A Gen 3 would definitely get better mileage simply due to being more aerodynamic. I'm not sure about 6-8 mpg better though. Plugging the numbers into our
aero & rr calculator, it looks to be a difference is more like 1-2 mpg.
The best way to increase mileage at those kind of speeds is aeromods hands down.