KH2's story for me has aged the worst with all the changes that happened within the series. Organization XIII is at the top of that list. I use to love this group at one point in time and I still love certain parts and the idea of it, but the whole Nobodies "don't have hearts" "don't exists" just never really made sense, even before the spinoffs. The games do a lousy job in showcasing why the Organization even need hearts, they function just fine without them. If they remember what it was like to be human then they can simulate it anyway. This has always been a big weakness of the Nobodies in how it's presented. In COM you have Larxene, Axel, and Vexen all reveling in their work and take pleasure in it. Sounds like folks who can feel to me. They are more lively then most characters with actual hearts. So where is the downside? Only Saix and Xemnas feel emotionless in tone and get that part down. Then you have "special" nobodies like Namine who is more of a ghost then a Nobody as she has no real body but is classified as one anyway, and Roxas who exists as Sora's dead discarded body while he has a new one but they have to merge because Sora's incomplete? So what was he at the end of KH1, a humanoid Heartless?
Part of me would be tempted to say, just rebrand them as Replicas. I still love the concept of Organization XIII and their members in the KH universe but just tweak it. Change the "don't exists" angle because if you can see it and it can physically hurt you then it exists. Replicas have that inferiority complex that could have easily translated to most if not all the Organization members, while keeping their core personalities in check without questioning if they have hearts or not. They have data artificial ones. They want KH to make a world without their real counterparts, so they still need the Keyblade to kill Heartless and make the KH moon. They go to Disney Worlds and try to replace the Disney characters with clones that they can control and manipulate Sora through familiar faces. The Dusk and other variants are Replicas that didn't take human form. This is obviously a "what if" scenario. I'm no writer and my ideas are the worst bad fanfics out there.
The reason I would rebrand them is because by KH3 Replicas basically replaced the Nobodies already. The most standout Nobodies were the Dusks, and the new fodder enemy designs. The fact that Luxord, Saix, Larxene, Marluxia, Xigbar, Vexen and Demyx were Nobodies was so unimportant to what they were doing you could have kept them human and the story wouldn't change beyond their deaths, which can easily be changed to defeats. Replicas on the other hand were huge. It was the Replicas and not the Nobodies that Xehanort used as backups for Scala. And they gave the Guardians more trouble then the actual Seekers of Darkness. They remain weird oddities given how they function and how they are created and what they do because it's all so unnatural.
There is more stuff I would tweak such as the "Ansem isn't Ansem" Roxas's overall story and conclusion in KH2, Namine and Sora's lack of a COM ending, and Kairi's role in general but this is already too big.