I never really thought anything in the main storyline was honestly ever THAT convoluted, assuming you actually played every game. I actually get confused at how other people seem to get so confused over it. Sure, sometimes there was a little bit of ambiguity here and there--and sometimes the answers to questions would change/expand as the characters (and by extension, the audience) learned a little bit more detail about a certain subject matter. And, granted, sometimes the writing introducing new stuff can be a little odd but so many key plot concepts are stated, reiterated, mentioned and explained again in other games, even written down in the Journal or narrative recaps for us to read over later that I scratch my head wondering how people miss all of that. I know I have a tad of an unfair advantage because I can understand the game in multiple languages which helps fill in some blanks now and again with translations but the game does explain things. Not well, but it does explain them.
I can understand maybe misunderstanding a concept or two but in terms of lore KH isn't "confusing" its just dense. Very dense and constantly evolving. And it gets entrenched in itself very quickly, so if you forget an important thread it can maybe result in confusion down the line because plot points are built on top of earlier ones.
It's just wild to me to STILL hear about people getting confused how there are "two Roxas' in KH3" or something similar. It can also get a tad frustrating when I hear someone say "KH is confusing", I ask why, and their reason is just "because it has time travel" (which is explicitly explained very directly in the game multiple times). There are many parts of lore that have not been well explained yet, or clarified so it's just odd to see that one come up so often instead of something currently unanswered.
It maybe sounds a bit strange to say but just because something is temporarily ambiguous, doesn't mean it is nonsensical and KH loves leaving things in a bit of an ambiguous state until it decides it wants to address them. If I don't really get something I just assume it's meant for later and move on/theorycraft until the answer is revealed and I have yet to really be let down in that regards.
To be honest in recent games there is actually very little subtlety in the writing in places I think could benefit from it. I worry that the reputation that many people perpetuate by saying the main story is confusing has made them go "oh shoot we gotta REALLY simplify this, gang!"
I always felt that KH was at its best when it left things more mysterious, and didn't fully write the rules out with stiff bullet points of "this is exactly how the lore works" which is what they started doing. Ironic that one of the few things they DO explain thoroughly with the rules and everything (like time travel) are the things I see people question the most.
All those complaints about the story being confusing are probably why we got that relatively needless explanation for how Mickey lost his shirt in the RoD.