She killed Obito and almost the the main characters. To be a decent villain you need to be a threat. Aizen was a threat due to his intelligence and Kaguya is threat due to her power. I don't see how Naruto's tactics working on Kaguya makes her stupid when they have worked on geniuses in part 1.How has she killed actually? I forgot who it was, but besides of that it does not really matter that much. Being a good villan is not only about killing. Aizen for example has not killed anybody, but he is still an amazing villan. To me and many other she is just boring and seems incredibly stupid. This is why I dislike her and hope that either Madara/Sasuke or (I know it s extremly unlikly) Orochimaru become the FV.
Edit: Aizen killed Gin.