Thank you for this. I don't it would be very realistic if everyone just liked all the characters. There needs to be room for you to notice the characters' growth by maybe having your opinion of them changed. There are a lot of characters in FF games I don't like but I don't see that as a game's bad point, since they need a variety of characters and it's impossible to relate to a wide variety of personalities.
Personally I think Squall is the best case of character development in any game. Tou can really see his growth because you always know his thoughts and can compare them with how he actually presents.
In FFXIII I didn't identify much with Lightning but I enjoyed her character's growth. For me the best character in FFXIII is Hope. Best development IMO.