This one is tough for me, I didn't hesitate for the FFX one, but here I just dislike so many characters that it's hard to choose. I pretty much hate Yuffie and she adds almost nothing to the story so she feels like a safe bet, but Red XIII is also a useless entity in the story as well. Sephy is a great backstory wasted on a generic villain and I agree that Shin-Ra should have remained the focus.

With all that said, I may have to go with Tifa, as she's largely connected to many of the reasons why I don't like the plot, and I've really grown to dislike her whiny, clingy, needy personality. The more I think about removing her from the story, the more I feel like the twists and turns in the plot would have worked better. Without her reference to ground Cloud's past, the story would have come across more interesting if the plot had just let Cloud's true past remain ambiguous.