This idea is courtesy of ColBlair, so I don't take credit for this idea myself.
Be that as it may, and although I personally believe Matt Reeves isn't likely to have had this in mind, in a way, Abby's clothes tell the story of her development.
When Abby first arrives, Owen (as well as us) notices her clothing. She's with Thomas, her hair is down, and her clothing is rather dark and shabby.
http://i7.photobucket.com/albums/y263/Bioroid/abbyclothes.jpg
Later, when Abby first encounters Owen, she is wearing the same dark clothing, but now she is hooded. In a way, this is a sort of physical representation of her shutting him out, along with the phrase, "I can't be your friend."
http://i7.photobucket.com/albums/y263/Bioroid/abbyclothes2.jpg
Same applies to the next encounter, where Owen performs an act of kindness by offering her the Rubix cube.
The third encounters has changed. Abby is no longer hooded, looks "cleaner," is smiling more, and even has gone to the trouble of wearing shoes. She is now allowing herself to be a friend to Owen, and this look follows through the rest of their "dates" on the playground, arcade, basement, etc.
http://i7.photobucket.com/albums/y263/Bioroid/abbyclothes3.jpg
This isn't the only time we see Abby dressed this way in a more "open" manner...
http://i7.photobucket.com/albums/y263/Bioroid/lolnerd.jpg
Despite her "Help, get this nerd away from me!" look, it's fairly obvious that she's allowing herself to be a friend to Thomas here too, in a very similar way that she is with Owen.
When she's first introduced, she's dressed in more or less the same manner. (Thomas himself also seems to retain a similar style of clothing later in life, which in a slight way introduces a contrast between himself and Owen.)
Owen and Abby take a turn in their relationship when her secret comes out. Following the confrontation at her apartment, Abby asks to be invited into Owen's home. Here, he could have either said no, and Abby probably would've left, but instead, he invites her in (after witnessing what happens without an invitation), and she's placed her life in his hands, something I'm personally not sure she would've done with Thomas.
Interesting to me is that this is one of the first time, apart from the bedroom scene (another stepping stone in their "relationship"), where Owen is not wearing his "space suit" jacket with Abby.
http://i7.photobucket.com/albums/y263/Bioroid/abbyclothes4.jpg
Next we're shown Abby's sort of "baptism" into a new life with the water imagery we're going to get in a similar way with Owen at the end.
http://i7.photobucket.com/albums/y263/Bioroid/abbyclothes5.jpg
Afterward, we get to see Abby looking happier than she has the entire film. Her demeanor has changed, she seems more like a child again. Many have noted she seems more "alive" here than she ever did with Thomas. Also significant is that her clothing style has changed. She was allowed to borrow any dress of Owen's mom, and she picked a very light one, which is in stark contrast to her previous way of dressing before.
http://i7.photobucket.com/albums/y263/Bioroid/abbyclothes6.jpg
For those that have scene the deleted scene, the last time we saw Abby wearing clothing in this particular colour... was the last time she actually was a child.
http://i7.photobucket.com/albums/y263/Bioroid/abbyclothes7.jpg
http://i7.photobucket.com/albums/y263/Bioroid/abbyclothes8.jpg
Later, when the policeman finds Abby sleeping, she's still wearing Owen's mom's dress. She's worn it the entire night.
http://i7.photobucket.com/albums/y263/Bioroid/abbyclothes9.jpg
Of course, even though she has realized she can be a child again, she has to accept that the vampire is part of herself now too, and we get the image of her in the dress, drenched in the policeman's blood.
http://i7.photobucket.com/albums/y263/Bioroid/abbyclothes10.jpg
Of personal interest to me here is that at the same time she is still wearing the dress, albeit blood-stained, Owen here is also no longer wearing his jacket... something he only does around Abby, at home, and in class, places where he's "safe."
Along with this, the blood on Abby's mouth gets transferred to Owen's, so now they form a sort of mirror image of each other. This also may indicate one possible course for Owen's future, to become a vampire himself. Unlike Thomas, who wore bags to protect himself from the blood he was shedding, Owen carries the blood of a victim on his mouth.
Abby, in one of her most human moments of the film, tells Owen she must go away, and when this occurs, we see two things: Owen is back in his space suit and Abby is back to her old shabby dress, ways in which they protected themselves from the world, but keep in mind, this is only temporary... they've changed too much to go back to their old ways.
So, in a way, the light vs dark motif of the clothing does seem to show a certain growth of Abby's character, and from this it's possible to gain a certain sense of hope that maybe, just maybe, things will turn out happily this time for the both of them.