BocoDragon
or, How I Learned to Stop Worrying and Realize This Assgrab is Delicious
You are flat out wrong about the novels, most of them shipped the same time as the film, and were deeply woven into the plotline. Not much to say other than you are wrong.
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There is very little of that "plotline" up on screen in the original cut of Advent Children. There's a disease, there are some Sephiroth clones, and Cloud is all emo about it. That's pretty much the extent of what is in the movie they spent years creating. You find it surprising that they were able to elaborate on it in short stories written long after CG development? I sure don't. And I think it's quite clear, based on the narrative present within the film itself, that plotting didn't dictate the character of Cloud. Cloud being mopey was a trademark Nomura aesthetic that they later justified with additional material.
To be clear, I am NOT saying that Nomura didn't set out to have a brooding character to begin with. He very well may have. But the way it is handled in the film and novels justifies this, as well as the events that take place in the later parts of FF7. Nothing is out of character, and everything fits, whether you personally find it a good design choice or not.
In VII, Cloud was a random, unspecial military officer, who only imagined he was a badass. He was kind of a loveable, clueless goof. He's often depicted in official FFVII art with a big dopey grin on his face.
In AC he's like an emo band rockstar doing Matrix movies. Brooding and posing like a 1990s CK ad.
"Nothing is out of character"?