Shion with every Xenosaga installment. Her design looked incredibly bland in II, and she looks like a space hooker in 3. Also special mention to KOS-MOS's lava lamp design in II.

Also, all the Persona 3 characters aside from Junpei are fashion disasters in P4 Arena.

I quite liked Sabrina's design, actually, but Wallace's in ORAS was just weird. I mean, all the other gym leaders got awesome new looks that made them look more islandy, but Wallace just went all-out Lady Gaga.

When it comes to redesigns I liked, I think all the returning characters look better in Baldur's Gate II, especially Minsc and Imoen.