Except that isn't true in the slightest. People have a hard time accepting it, but Nomura has had a lot of this story in his mind for a long, looooong time. There are things in the first Kingdom Hearts that are hinted at which he won't expand on until, like, in Birth By Sleep. And ever since the introduction of the Organization XIII, there have been clear hints that there's more to them than meets the eye (I mean, they are looking for something in Castle Oblivion in Chain of Memories, yet to fully understand what Castle Oblivion even is and what they are looking for, you need to play Birth By Sleep, a game that was release 6 years afterwards). Nomura pretty clearly hints at a lot of stuff during even the earliest games and none of the follow-ups to those hints feel like he's just making shit up.
I mean, sure, realistically speaking of course he hasn't had ALL of the smallest details thought out 10 years in advance, but he has had some rough ideas of a lot of things. There's some flexibility to some aspect, so people like Axel have likely gotten a bigger role after people came to like him so much, but I really do believe that he has had the whole Master Xehanort -> his incarnations & evil master plan with Org XIII and the Ven/Sora/Roxas deal more or less thought out ever since Chain of Memories, when he got the green light to do sequels to Kingdom Hearts after the first game was so successful..