I think most people can agree that Revenge of the Fallen on its own merit is clearly a worse film than Crystal Skull. However, the subject of this episode isn't which is the worst film. The subject is which is the worst sequel. The criteria you laid out in the beginning fits Crystal Skull perfectly. It makes the most sense that the more beloved the franchise is, the more heinous the existence of a bad sequel. The first Transformers movie doesn't have anywhere near the same beloved fanbase, people who have spent decades watching these films, studying them, analyzing them. Film students study the Indie movies, the tropes that they exhibit, the inspiration and history behind the adventure serials their film style is based off of. Transformers has always been the subject of criticism with fans from film one.