The series' ideas about gender (and race) evolve somewhat as it goes on, if that helps any. Volumes eight and nine have storylines that seem to be intended as criticisms of the male characters' (particularly Ido's) need for Alita to be vulnerable and feminine in volumes one and two. I mean, the manga never ceases to make choices that irritate me, but you can see the mangaka questioning himself and changing things. One of the things that fascinates me about the series is how visible it is when he decides he's done something stupid. The biggest example of it comes when he realizes he kinda has a lot of racial stereotypes in there. Yukito Kishiro's complete lack of subtlety is an eternal inspiration to me.

(He actually gets a little too self-analytical sometimes. I'm beginning to suspect Last Order, the sequel series, of being some kind of massive self-parody. I can't come up with any other explanation for the last couple of volumes.)