Two notes:
Derek, you raise an interesting point about what makes Naija such a fascinating character. While obviously Lara and Samus are entirely different beasts spawned from vastly different creative centers, one being an oversexed adventure cliche and the other being a near-silent agent of contextually emotive storytelling (can you guess which one I prefer?), Naija's innocence and -- most extraordinarily -- her sense of wonder set her apart in alarmingly unique ways. My sense of alarm, I think, stems from the sheer lack of this sense in other characters around the gaming spectrum. When Naija offers a soft gasp of surprise, or a quiet little "wow" of fascination, I'm awestruck at the power it has to help convey the physicality of the world, the inherent (if sometimes merely implied) nature of it. And that's cool. As hell.
Which brings me to my second note. I think that sense of grandeur is what made me feel, when playing Aquaria, similar to how I felt playing ICO and SotC. Not because the gameplay is at all similar, but because there was that sense of something wondrous. The games all achieved it in different ways given the different storytelling methods and natures of the protagonists, but all 3 games were palpably wondrous to me. I keep using that word because I can't seem to find anything that better describes the feeling. What Aquaria may have lacked in terms of dimensional depth or raw GPU-pushing technology, it made up for in art, sound, and a pervading sense of carefully meted mystery. Of obfuscation, even, but only when that lead to making something more interesting or intriguing instead of merely more obscure. All 3 games excelled in that regard, and the sense of wonder was present as a result. But in Aquaria's case, it was most uniquely expressed where it seemed to emanate from the heroin herself, and that made a huge impression on me. Identifying with her was easy because of that, and the sort of humility present in that attitude is what makes her so heartbreakingly fragile, so disarmingly endearing.
I wrote a long review of the game when it came out, just so I had a link on my own site to throw at people that I thought would like the game and because I really wanted to see it succeed, but I don't know if I'd exactly realized how far the emotional connection with the game extended until I had some more time for reflection. I knew partly why I was connected, but I don't think I quite understood how Naija's connection to her own world affected my own connection to it; and not just because she was there swimming in it, but because she and I were both equally stimulated by it.