By book five, Cersei is a much more developed character than Varys or Littlefinger. We don't understand at all what Varys or Littlefinger want (and Martin has confirmed they will never be viewpoint characters because "they know too much"), but Cersei's thought processes are clearly and thoroughly documented out.
I really don't think the depictions of rape in the series are generally gratuitous. Martin may be a fantasy author, but he's striving for realism as much as possible (he's stated this explicitly several times). Rape happens a lot in war. Rape happened a lot in medieval history. The story depicts a medieval setting which is largely based off our own history and happens to be in the midst of a brutal war.
That's not to say there aren't instances of it where it's lazy writing, but I don't think for the most part that he is using it because he has nothing else to fall back on; he is using it because it is what happens in war. It is not as if Martin shies away from other atrocities, either; the horrific tortures inflicted on others by the Bloody Mummers (which, admittedly, include rape, but go far beyond it as well) are proof of that.
And The Mountain had no reason to rape the inkeeper's daughter? When do rapists ever have reason to rape? Most rapists are serial rapists, which is a fact large numbers of people seem to forget. If you depict a person committing rape once and then never doing it again, that is not a realistic depiction of what usually happens in real life. I would say he becomes much more vile because he keeps doing it over and over. This is another reason real-life rapists are so vile as well.
It's crude, it's brutal, and it's not even remotely subtle, but that's the point. War is crude, it's brutal, and it's not even remotely subtle. If people had any idea what war actually entails in real life, it wouldn't happen so much.