I don't know, I hate every anime or film version of anything Shirow ever wrote. The slightly better characterization is not enough to pay for the massive losses in all other areas. Regardless of his other failings, Appleseed v1 and v2 and GitS 1.0 were some absolutely brilliant Sci-fi by any standard, not just manga or comics. And I'll always have a big ole soft spot for the sheer hilarity of the Tank Police.
By his own admission, Shirow is a bit of an antisocial nitwit - then he caught too much of the Kenichi Sonada Fetishist disease. The last two books of Appleseed were basically an exotic feild guide to commando tactics with an occasional gag reel thrown in. And don't even get me started on the GitS 2.0 manga, Jesus H. Fucking Christmas what a waste. I want to see Appleseed finished someday, but I'm still afraid to look.
I know Shirow was always balanced on the knife edge, but oh how far he fell.
***
Anyway, tangeant aside, the real problem is that Shirow's one of the thousands of dorks (asian and non) who write female leads not because they think their story should have a strong female lead, or because they beleive in equality, or empowerment or whatever the fuck, it's because that shit gets them going. That's not to say that ALL instances of female leads with poor characterization are because the artist is randy for his creation (though that does happen), it can be as simple as wanting to draw girls all day instead of guys.
I'm not one of those hardcore pro-equality guys who collar and leash themselves and spend their days denigrating men, but I like to see both genders properly written. I think the recently mentioned Planetes* did a decent job there, especially with Fee. North Americans are hardly immune either. That's why we see shit like the Wonder Woman debate. (You're telling me the ONLY way anyone can think of making a female lead strong and distinctive is to make her into a lesbian? really? Are they seriously that fucking clueless?!).
Back to Manga, another book I think of where the females are done in a decent way is Blade of the Immortal. Rin is fairly cliché at first, simpering and useless, but she really grows over the story. The current arc has had her out of Manji's shadow so it has really showcased a lot of changes that were subtle and may not have been observed along the way. Hyakurin is also a good example of the cynical doyenne who's not so old that she's 'lost her stuff'. That can be pretty hard to write without making the character too slutty, too cold, too soft. I'd say Samura does a pretty respectable job. But he was good with female characters back when he wrote short romance manga, so he seems to have the knack.
There's not much more I can think of besides that.
*I wish I could get more Manga like that, but I just can't be bothered to wade through the rest to find it anymore. Most of the shit I have now is pretty damn old.