This was why I don't follow KH. It's confusing and it gets worse midway through
KH, as a whole, is not well written. But KH1, KH2 and the DS spin off had good character moments that made you care.
KH2 especially started out with a really nice bittersweet story of Roxas not wanting to merge back with Sora, trying to fight against that fate until he can't. It's sad, but you also see that Roxas is part of Sora now and you get moments like him shedding tears when saying goodbye to the real version of his friends. Near the end Roxas truly makes peace with it after fighting Sora in one of those anime mind battles, being content with the fact he's a part of Sora now.
Now, given this storyline, what is the one thing you could do to completely fuck it up. You have a plot point about the KH crew giving the Nobodies their own bodies. This is extremely retarded and completely undermines the above, but you can make it worse.
The DS game with the retarded name was a shit game but actually had a good and tragic plot that hinged around a character created to fill the role of keyblade wielder. The fact that she exists to be a tool and nothing more is played for full tragedy, because she forms a friendship with Axel and Roxas and gets to actually be herself. But eventually her role causes her and Roxas to fight and Roxas is forced to kill her, with the kicker being that because of what she was everyone's memories of her will be erased. Roxas promises not to forget but can't fight fate.
Now, if you wanted to completely ruin the above what would you do? You'd somehow bring said character back and restore everyone's memories. The whole fucking plot meant absolutely nothing.
And the kicker is Nomura didn't even want to do either of these but was so badly buck broken by Final Fantasy XIII Versus that he mindlessly catered to fan demand to do both of the above.