Great Characters - Despite Gender

Let's have a chat about Gamergate. Just kidding! Don't worry I won't bore your ear-holes with more of that drivel. However, I would like to take the topical nature of the subject in order to mention some of my favorite female characters. Now these selections aren't meant to feature strength or even be anti-sexist selections. They instead exemplify well-written characters and also represent their gender in a more-or-less accurate way. 
I want to highlight two characters from games I have personally enjoyed. This is to say, I am not making a definitive list, nor am I excluding anyone. I am simply outlining 2 good examples. 

Samus (Metroid):

I am going to take a moment to push my own personal agenda. There is an elephant in the room. Metroid the Other M and its depiction of Samus as a character. Before The Other M, Samus more or less lacked a voice. Apart from stilted text boxes, Samus was a silent hero. However, this doesn't make her a strong female, or even a good character. Strong, sure, but anyone can make a strong entity that overcomes all obstacles. It is in the small moments where you see real character shine through Samus. The strongest of these is during the climax of Metroid II. Samus has dispatched the last of the metroids. During her escape she encounters an egg. As it hatches, the metroid inside is instantly bonded to Samus. Hinting at motherly affection, Samus stays her hand. Identifying with the orphaned metroid they make an escape. This is a decision, it shows emotional depth. It is a decision arrived at from Samus' past experience. It shows a soft side and that she is capable of thought beyond being a shell for the player. 
The Other M plays into this- justifies it. By delving into Samus' backstory: the struggles she endured,  her relationship with superiors, and her feelings for that baby metroid. You gain insight to why Samus is the way she is. The Other M frames Samus' state of mind. Yes, sure it may show her in a weak light. But is that bad? Samus has proven she can take of herself. She has shown her strength. Her own foibles are where she draws this strength from. It shows she has depth. That she can be motherly. That she is a badass. And most importantly, that Samus Aran rules. 

From metroid.wikia.com

Ellie (The Last of US): 

Ellie will probably be the most important entry to this list-thingy. Both her gender and age play a strong role in the narrative and define both her actions and interactions. She is a teenager in a world that has fallen to ruin, Ellie is a new generation burgeoning into this new life with no pre-bias of what society is. She has the potential of a blank slate. As she grows and travels with Joel, she learns what she can do- how she can help. As the relationship between her and Joel develops it you see her desire for fatherly support, not only to protect her, but to help rebel against. Joel allows her to prove she is her own person who can take care of herself, but he also teaches her and shows her the way. The dynamic between them echoes a very Freudian style. Her feminine nature affects Joel and changes the way he sees the post-apocalypse.  It is hard to capture the absolute shit-storm of puberty. Naughty Dog has done a fantastic job, and allowed her gender to play well into the narrative and her character. 

From cdn2.omnigamer.com