This is an interesting question, as it's basically asking a different question from "What is you're least favourite" to "what Game do you think affected the FF series the worst?"

It's a harder questions than most. As every FF game has some merit.

I'd probably say the FF 13 series. Not because I dislike the games, but because of the fact that they could have worked on other games and new stories, but stuck to one universe and set of characters for 3 games.