I would say by far the biggest misconception of the series is how densely complicated and impossible to understand it is. Part of this is rooted in a kernel of truth—the series IS very lore-heavy and keeping all the information straight can be difficult, and that's before you introduce time travel and parallel worlds into the mix. But I think the series' reputation for being impenetrably convoluted is largely a smokescreen created by the fanbase itself. I think at some level the fans of the series enjoy playing up how complicated the series is to normies, maybe because they feel insecure about liking a Disney game meant for children and feel they have to justify it by emphasizing the intellectual rigor of keeping up with its lore, or maybe it's a gatekeeping thing, or maybe some people just feel like they need to over-prepare newcomers to get them ready to pay attention to every little detail.
But overall, I don't think the story of the series is that complicated. What makes it SEEM complicated is the fact that a lot of information is not presented clearly, and a lot of information just isn't presented at all, which can lead to confusion and inconsistencies. There's a big difference between the ambiguities in Kingdom Hearts, for instance, and the ambiguities in games like From Software titles, where the ambiguity and lack of information feels like an intentional part of uncovering or comprehending the narrative. But with Kingdom Hearts, it really just feels like Nomura writes stuff in that he doesn't really think about, and then either forgets about it or comes up with some retro-fitting convoluted explanation later when he make it conveniently tie into the current narrative.
At the end of the day, Kingdom Hearts is just a series about a boy and his circle of friends trying to stop the universe from falling out of balance by keeping the darkness at bay. That's really the long and short of it. Everything else is just window dressing and getting from point A to point B. And I think fans tend to fool themselves into believing it's more intricate and sophisticated than it is, or they just get a kick out of making outsiders think that to counterbalance the whole kid's-game vibes.