I've never had Whiterun completely restored after the CW and I've only ever done the Stormcloak side. The trellis around the Gildergreen still remains beaten up, Severio Pelagia and Heimskr's houses still remain destroyed, the small (unused) guard post near where the Khajiit traders camp still remains a pile of rubble, and the walls still remain battered. I just get used to it after awhile.
The thing I hate most about the CW quests, though, is:
Spoiler That the guards all end up wearing Stormcloak uniforms instead of their hold uniforms, even if their hold was allied with the SCs to begin with. I miss the variety!