This was a great discussion, so glad to see so many of my own beliefs being mentioned. I love that they actually defended Lara Croft, since I've personally had someone ask why I don't hate her. I never used to be big on her, but regardless of appearance she's not a bad character. She's the female Indiana Jones, a series I love, and has had some damn fine games. In particular Guardian of Light is a BLAST.
I sorta agree and disagree on the discussion about Yuna though. If you only count FFX, she was a decent character, but FFX-2 screwed that up. But if you want to pull an example from FF, and this one more so shows why Lightning was awful, is Ashe. She wasn't helpless, she wasn't a badass. She had to struggle with what she wanted for herself and what she needed to do for Dalmasca.
As for the discussion about how characters, not just females, need to be characterized better, and someone said they wanted to see a game where it was well done, I can only say this: Half-life 2. Well done females in Alyx and Mossman, and there are OTHER RACES without ever calling attention to it. Yeah, there are no noticeably gay characters, but that's one that's really hard to pull off without being offensive, as if it's done right you have no idea at all. For all we know Barney could be gay, as he seems to have a sort of man crush on Gordon. And if he is, it's never clearly stated, which is one of the best ways to do it.
Oh, and super thumbs up for mentioning Howl's Moving Castle. Easily my favorite Miyazaki film next to Princess Mononoke.