I think the odd thing about the complaining is that the Agent Carter bus, at least, is far better themed than the ordinary buses. It makes the ordinary bus look like something distinct and interesting. While it may be an advertisement, IMHO it is one that actually enhances the environment.
Beyond that, I don't see how doing the wraps or not damages the WDW experience. The buses are not "on stage" and part of the theming and environment to begin with. I'm actually sympathetic to most arguments about intrusions of the outside world into the theme parks, but this strikes me as an odd place to draw a line.