Ilosar
Vault Fossil
The Ace Attorney Series (5 games)
Thhe games with the little girl turning into her mature sister, but keeping her small clothes? The game with a whip-toting crazy lady? I am not so sure.
Persona 1, 2, 3 and 4 (with a huge variety of characterizations per game)
Can't comment, never played.
Fallout 1, 2 and New Vegas.
Granted. But then again this is Black Isles/Obsidian we are talking about, I would be dissapointed if the best writers in the industry (imo) ere to fall for such cliches.
Infamous 2
...Yeah I guess. There's not much character development IIRC, but they do influence the story somewhat.
Planescape was covered.
Catherine
Ooooh boy. That one is really hard to say. Some think it's gender-equal. Some say it portrays men as assholes. Some say it portrays women as either overprotective bitches or dreamy, slightly idiotic minxes. The box art and slightly exagerated character design does not help.
Portal 1 and 2
The only human female in the series being mute? That's like saying Gordon Freeman is an original, strong, believable character. Except we know nothing of him save that he can kill armies by himself.
So yeah, off the list I can grant 1, maybe 3 if we strech it. You could add various Bioware games to it, I assume. And I could name 5 too. they are not SO rare. But the fact remains they are largely the exception rather than the rule, or at least the standard.