Some plot points thrown in can confuse us but I think if people play all the games and accept everything that was presented then the story isn’t really at all convoluted. Obviously missing a game will create confusion but that’s a given. I don’t think the story itself is convoluted as most people see. It just makes you think back and try to see if you miss anything or not. Make no mistake though, it is convoluted in nature but once understanding it then it isn’t.

Another note is that I think the sentiment comes from people trying to explain the story to a friend who's never played the KH series and shows zero interest in it, but the teller can be seen as getting way too ahead of themselves and tries to explain everything all at once when experiencing the games for yourself is the best possible immersion for someone to get to know the story.

I’ll give an example which is the infamous Ansem identity:

There have only been two Ansems if one looks at it, at the premise of KH1, the plot twist of Ansem being the evil mastermind is revealed, CoM even hints at the two Ansems when Riku talks to Vexen. The plot twist of the real Ansem - Ansem the Wise - having his identity taken by Xehanort, whose Heartless kept calling himself Ansem was revealed. Arguably Xemnas can be seen as the third Ansem due to his name being simply an anagram of Ansem, Riku too who used the name Ansem when he took on the fake Ansem -Xehanort’s Heartless - appearance.

So really that’s all to it, it’s not like there’s more of a mess to that whole Ansem identity convolution.