Let's see if I can think of some. Most games you will see in the good and bad list

Bad:
*The Rikku one I agree with. I much preferred her look in X over X-2
*Shion got worse from game one. I'm in the minority though but I liked her II outfit the least
*KOS-MOS from I to II was awful
*Rorona from Totori in to a 6 year old was awful in Meruru
*Not a fan of Julia from Tekken IV+. I like her look in III the most
*The middle games of Mortal Kombat made most characters look gosh awful
*I haven't played the Persona Arena games but the character designs turn me off
*The one that started this thread: Alice from Bloody Roar. She has a similar design in the first three games and in the fourth she looks like a completely different person. The character looks fine but it doesn't look like HER anymore. Nice outfit though
*Milla in Xillia 2 is bleh
*Jeane in Suikoden V was a step down from the rest of the series
*Most of the character designs in Soul Calibur IV

Good:
*I loved Penelo's redesign in Tactics A2
*KOS-MOS from II to III was good. I like how they took a design similar to II and then killed her off (ish) and brought her back in a look more similar to her first one. Honestly though I like both in III and I obviously like her outfit in I
*MOMO I think looks the best in III compared to I and II
*Chaos also ditched the awkward short shorts
*Rorona from Atelier Rorona looks batter in the later Totori, I find
*Xiaoyu from Tekken 3 improves every game
*The newest Mortal Kombat has done some great things with the characters, especially Mileena and Kitana
*I like Athena in KoFXIII above most of her older designs
*Luc in Suikoden III is a step up from marshmallow wand

Uhh those are the ones I can immediately think of