One problem I thought of in planetary incursions would be that shields don't work. Shields (are supposed to) convert matter or energy that impacts them into diffused photongs (light), which is what causes the nice flash every time you hit something with a shield. Think that in the atmosphere, a shield would constantly be draning it's energy on the molecules in the air that are impacting it, which would make shields ineffecitve.
Of course, in FS, shields are selective - they stop weapons, yet ignore other ships, asteroids, and beams, but who said FS was realistic?