Are there any villains who are pure evil and rightfully so, but end up, due to reasons such as a lack of screentime or not having their character or goals developed enough, having you mistaking them as a Generic Doomsday Villain?
For me an example would Ozai. Despite having a few notable crimes, he is ultimately the Bigger Bad of ATLA due to his children instead being the main threats to the protagonists. In addition, it is never explained why he is such an awful father except that he happens to be evil. The film version is an even larger example of a GDPE.