Hall of Fame:
I wouldn't Shepard since that's a player-proxy and not really a character. i would trade her for Elly from Xenogears. Despite how terrible (and dare I say exploitative) 3rd Birthday is, Aya still deserves to be on the list. Still, a VERY good list.
Honorables:
Again, a very good list. I still need to play all of BG&E. And thanks for the mention of Samus.
Shame:
Oh. My. GOD. I HATE Shion with a PASSION. Not only is she a terrible, emotionally unstable, manipulative, whiny, pushy, petulant, arrogant, spoiled, self-entitled -insert expletive here-, she also CANNOT justify her existence in the storyline and she's BORING. And I STILL can't believe it since the series' spiritual predecessor had Elly who is one of my favorite female characters and her story with Fei is actually IMPORTANT. Shion has NO reason to be in that plot and practically every other character is INFINITELY better written and more complex than she is (seriously, Ziggy, Jin, chaos, and KOS-MOS should have been the entire cast). Either the writers just blew themselves out after one game or it wasn't just them that contributed to the story (and since Kato wasn't on 'Saga, I can't help but be suspicious).
The Star Ocean cast I can't blame them for, but I did like them. I also disagree with Peach, but hey, I guess I can't blame them.