This is a deconstructionist argument gone awry. You're basically saying that Valve manipulated the players by crafting a female ally who isn't a complete *****.
The truth of the matter is that a female companion who shows ANY affection for the player, whether it's physical or emotional, is going to boil down to player manipulation on the part of the developer. Because she's not real. She's a nonthinking construct.
Yuna's no different. Her journey, her growth, all that? Artificial, and therefore manipulative.
That's kind of the point of videogame stories as well as film and literature - to manipulate the viewer's emotions. Some do it better than others, and Alyx is by no means perfect. But hating on her design because she fits the far healthier and more intellectually/emotionally engaging stereotype of "the thoughtful girl next door", rather than the badass sexpot or psychologically imbalanced wounded animal, seems... backwards.
I liken it to the rift between dog and cat people. Cat people like to hate on dogs as emotionally shallow animals because they're broken, dependent, and obedient to a fault. Dog people laugh at cat people because they're catering to the whims of a little ungrateful shit. The truth is that all relationships involve some amount of manipulation, and classifying it as good or bad is something you have to leave in the hands of each individual.
Me? I'm a dog person. I dig Tali and Alyx. I don't think being supportive, modest, and approachable makes a girl weak, and I don't think being attracted to those traits makes me weak either. Some of us aren't looking for drama, negativity, pessimism, sarcasm. Some of us don't subscribe to "opposites attract!" or "sparks will fly!". A lot of people go for the nice girl next door because that seems like a sensible route to a happy life. If Alyx preys on that "fantasy", so be it. That's a respectable fantasy worthy of encouragement.
I'm a dog person. I dig Tali and Alyx.
Whoops.