I've always seen her as an avatar for me to inhabit, although I must admit that I see most video game characters as such. I have a way of focusing more on the world around me/the character than on the main character him/herself. I suppose this is why Metroid Prime (and its sequels) pulled me in as a player with ease. Samus could have been anyone, but more importantly she allowed me to be, well... me. I explored the world at my own pace, took in the sights and sounds. Battled the monsters, saved the day, etc.
Playing Super Metroid/Zero Mission really was no different either. I was Samus, and Samus was me. I'm the one that explored Tallon IV and took down the Space Pirates and Mother Brain. The story explained in text at the beginning and end made little difference for me.
So yeah, I think little of Samus outside of the games in which I play as her. I do the same thing for Mario, Link, Donkey Kong, Sonic, and a multitude of other characters. For the most part, they're avatars for me to fill and explore the worlds they were made for. Sure, in some cases (like Samus I suppose), it's not what the creator of the series intended I did with the character, but ya know, it works for me. *shrugs*
