Kingdom Hearts has some insanely convoluted games (Coded, Dream Drop Distance) but I think for the most its relatively simple to understand, and, aside from the afformentioned entries, I think that the game's internal logic is fairly consistent.
The main issue with KH has always been how scattered it is - basically each game is important yet the game kept jumping between sony and nintendo consoles, but not even that, it also kept switching between home and portable consoles. And the compilation largely solves this, but, not entirely, since it takes quite a lot of willpower to slog through Chain of Memories' gameplay for instance or even just sitting through 4 hours of Coded cutscenes... oh boy.
But I digress, I think for me the afformentioned Black Ops 3 takes the cake. I don't know why anyone thought it was a good idea to put such a complex, hard to follow plot in a CoD game. But to make it worse, they decided to do it in the instalment that has 4 player coop support - reading the mission briefing and lore documents is absolutely essential to even begin to understand wtf is happening or why, but doing that in coop is almost never gonna work out.
Like.... I honestly think less than 1 % of the players are aware that "you", the "player" character is actually dead during the entirity of the campaign. Which is never actually revealed, not even hinted heavily. It's just.... written down.