A couple of other suggestions:

• Heat generation when using thrusters in atmosphere
• Even more heat generation when hovering/slow-flying at non-ideal angles (i.e. when using retro-thrusters to fly with the nose down)
• Eventually thrusters will stop working / take damage due to excessive heat (ground, meet spaceship).
• Shields could make rovers actually survive a few hits
• Stealth mode that makes them really difficult to find and track from the air
• More in-atmosphere anti-air weapons (i.e. heat-seeking rockets) to deter potential aggressors.

I feel stealth would be really useful on non-atmospheric / low gravity locations as well; it gives you a reason to actually land your ship and use the rover if you don't want to be noticed. It also gives you a safe way of escaping other than running away. And stealth could again be partially countered by sensor designed for that purpose (i.e. dedicated scanning stations on larger ships).

Stealth-mode should also have a cost associated with it (i.e. lower max energy drain / no shields / no weapons).