Kabuto's main problem, IMO, is that Inoue just didn't work well together with Yonemura. As soon as Inoue arrives in the show, there's a clear change of atmosphere that carries over to Yonemura's episodes. I thought the show was still enjoyable afterwards, but I don't think Yonemura ever handled the new atmosphere as well as the original one. The worst part though is how they wrote the same characters differently. Everyone's voices are very weird in Inoue's first two episodes. The later ones kind of fix that issue, but the two writers still clearly wrote the characters differently.
Yonemura treated Kabuto as a distant protagonist whose actions were mostly observed by others, aside from a few very personal circumstances involving Hiyori. Inoue wrote Kabuto as the standard point of view character. Initially, Inoue also seems to regard Tendo's sayings as a bunch of nonsense, with Tendo even eventually explaining himself at the end of an early arc. That issue disappears in his later episodes though.
Yonemura wrote Kagami as a promising young man with lots of potential but lacking focus and knowledge, often relying on various others, leading to bad decisions, until he learned how to stand by himself in the final episode of the series. Inoue wrote him as Kabuto's hotheaded sidekick.
Inoue wrote Drake, Yonemura at best seemed to get to write scraps for him considering how his actor was never around in his episodes.
Inoue wrote Tsurugi as Tendo's rival and mirror, in his introduction to his departure from the series. Yonemura wrote Tsurugi as a lovable buffoon who befriended Kagami and developed thanks to him (which stands in stark contrast to Inoue penned ending arc where the entire focus of his character suddenly changes back to Tendo).
Kabuto vs. TheBee was a typical Inoue Rider conflict, and it was actually pretty good.
But Kabuto vs Drake and Sasword? That was clearly Yonemura's doing. Forced conflicts that had nothing to do with the overall story and were only there to make action scenes.
Inoue hadn't even touched the show by the point of TheBee vs Kabuto. He only started writing for Kabuto with Drake's arrival. In fact, almost every single arc that featured Drake's actor was written by Inoue. In some later Yonemura episodes of Kabuto he had to do things like Gon speaking for an off-screen Drake or even a suit only Drake once.
Wikipedia has a list of who wrote each episode:
http://en.wikipedia.org/wiki/List_of_Kamen_Rider_Kabuto_episodes Look at KR vs SS. It suffered the exact same problems as Kabuto, because Yonemura couldn't handle anything outside the battles.
Super Hero Taisen was a big exception in a sense though. The previous Yonemura written crossover movies generally didn't have nearly as much focus on action or random past heroes as they should. Just look at Let's Go Kamen Riders, where the other Riders only arrive for an ending scene and mostly just stand in the background there. Even SHT really should have used more past heroes. Still, I thought it was an evolution in a sense - since it seemed to use the "all" crossover element for the entire story rather than just a battle scene at the end, even if the story itself was fairly empty.
Of course, in the end, it seems like SHTZ changes right back to the format of the other movies, only focused on featured series with the other heroes just randomly appearing for the final battle, so, SHT seems like it'll be just a one off.
I really hope they bring different writers for the next movie, since it seems like he's stuck in that format for crossovers. Although maybe the other writers just don't want to work with Shirakura...
