Biggest problem of KH lore is the same thing that MGS suffers from, everything has to be connected to past games and characters because of reasons. It makes the world of these games much less interesting and makes it feel like the main characters live in a bubble.
Chain of Memories was the last game that introduced new original characters that (at the time) felt weren't forced to have these ridicilous character arks that need to have a connection to characters in KH1. Namine for example I feel was way more interesting and better character in the original CoM before they revealed her connection to the old characters. She would have been much cooler just being a witch with some mystery to her, everything doesn't need to be explained. Remember when ''the superior'' was this mysterious being that made organization members shit their pants before he was revealed to be a boring rehash of the first villain because of reasons (Xemnas is by far the worst big villain in KH). Remember when Axel was a psycho?
The lore is still a guilty pleasure of mine and I don't mind the ridicilous elements one bit. I just feel like it could be so much better. I don't mind overarching story elements but when it creates a web of connections like this it just diludes everything down.
Honestly, the biggest issue isn't the connections. That I can deal with, and if it means a better payoff to the long arc, then I'm all for it. The big problem is HOW those connections are made. And then how you, as a player, are supposed to uncover those connections. Most of which involve encountering secret bosses, and in order to stand even a remote chance against those, you have to grind. And fuck grinding in any of these games, save for KH2, but only because it's far more bearable in that one. Lingering Sentiment in KH2 and the Unknown in BbS are examples of this.
A lot of it is also Nomura (and whomever else is writing this) believing that he (they) is (are) so deep and philosophical. Bogging everything down in repetitive word usage which is constructed in weird, convoluted ways. Ultimately it always boils down to "Light is good, dark is bad. But not always. Sometimes nothingness is bad, but then it becomes light. Or dark. We don't fucking know. But light can erase dark if it isn't swallowed by the dark nothingness within all of our hearts."
For me it's always been more of the "how" than the "what" when it comes to this series. But then again, I play these games for the gameplay and not the story, so there is that.