Shion from Xenosaga. Oh dear god I hate Shion SO MUCH. Almost everything she says and does fills me with rage. How an oblivious, passive-aggressive ***** like her got to where she is, and how everyone else puts up with her, is utterly beyond me.
Elly from Xenogears. She comes across as a total Mary Sue to me, especially the way all the other characters treat her--saying she's beautiful, telling her she has all this power that no one else has, blah blah blah. She's whiny and stupid and needy and useless. And for the record, I don't like Fei much, either.
I also have a general, all-encompassing hatred for the submissive, overly-feminine, doormat White Mage female lead archetype that is in almost every JRPG. Yes, this means I don't like Aeris. The two characters in this archetype that I DO like are Yuna (but only in FFX; her FFX-2 incarnation just makes me facepalm) and Alice Elliot from Shadow Hearts, mostly because they have actual personalities beyond just being arm candy for the male lead.
Oh, and speaking of Shadow Hearts, I also hate Karin Koenig from Shadow Hearts: Covenant. She's supposed to be a soldier, but she's just as whiny and needy as Elly and does not exhibit any of the personal strength that I expect from someone in her position, plus I hate how she constantly clings to Yuri like a leech. It's a shame, because I absolutely love everything else about that game.