I test drove a Prius C at the auto show last weekend. I was actually surprised at how smooth and comfy it was. Even at 46mpg highway you're still getting nearly 10mpg more than the Hyundai. As was mentioned, anything over 60mph and your hwy mileage is going to suffer, no matter what you drive.
The hybrid drive doesn't really have a drawback on the highway. At those speeds it's operating just like any ICE vehicle. Just in the city it can use the electric drive to get your momentum going, thus the better city MPG.
For a commuter with that many miles per day, you're going to have a hard time finding something that will get better MPG than the C. A TDI would get more mileage, but as you said, will have a higher entry cost, and cost only slightly less in fuel with the premium price of diesel.