Go for the hitch rack.
1. Nothing touches your paint or glass.
2. No worries about forgetting the bikes are on top of the car and driving under something low hanging or into your garage.
3. The wheels can remain on both bikes.
4. You don't have to lift either bike so high, which your wife will appreciate.
5. Less aerodynamic drag, less noise and less effect on gas mileage.
6. Easier to install and remove
7. Can be secured against theft with a locking cross pin for the rack and a cable securing the bikes to the rack
I have had both types, roof and hitch, and the hitch rack wins on all counts.