I don't want to single out any one person because I don't know who did what on their team, but there are some big flaws in story-telling and someone chose to do them:
They could have just left all the various untied threads from the handheld games alone and built a new narrative on top of them. We didn't need a single Organization 13 with a million bosses and weird stories. Instead, the game could have just been about fighting a single big bad who might be helped by some Disney big bads who have the advantage of having films made about them so that we all know their stories. We didn't need the 7 guardians of light or the 13 hooded figures of bad plot construction. It just isn't necessary and it doesn't lead anywhere.
The dialogue and especially the jokes were poorly written. Someone wrote those and someone green-lit them and allowed them to be animated and acted.
So I'm not going after any particular person. I think Squenix needs to make changes that stop them from repeating these same mistakes over and over though.