Without having seen it, I would assume it has to do with how good the writing is. It might seem natural in its context, but if it’s not handled well it might just as well come across as fan-service albeit one with better backstory.
For example, in the Sopranos the viewer is exposed to naked strippers pretty much every time the story takes place at the Bada Bing. In some other series or movie it might have across as wanting to show naked strippers just for the sake of it. Maybe there is some of that in the Sopranos too. However, not only does it make up for a big part of Tony Soprano’s character, but there’s an episode that shows the tough and abusive lifestyle of the strippers themselves, which puts it into another light entirely. In the end, it doesn’t come across as forced.
As for your question: is attractive female character design alone an example of misogyny or objectification? I say no, depending on how you define attractive. But couple the attractive design with genuine good characteristics and story (i.e. not constantly put down or outdone by male peers, not having her clothes torn apart for no apparent reason, etc) and it should be perfectly fine. The character Joan in Mad Men, for example, definitely has a sex appeal and knows to use it, but she also has intelligence and integrity. My girlfriend thinks she is a super woman.
GITS is interesting in this regard. In the first movie, the main character disrobes upon entering a combat situation and wears nothing during, as the “skin” of her cybernetic body is a high-tech stealth suit. Shameless fanservice for brief moments before she spends the entire following segment as nothing more than a faint outline. As for choosing the female body because of being originally female…the story (at least as far as I’ve seen of it) is ambiguous about that. It’s suggested more than a few times that the choice was because of it offering the ability to exploit chauvinistic males in undercover operations. That’s the only time she behaves in a sexual manner at all, and is otherwise stern, cold and aloof. Despite spending a large portion of the movie completely nude, she’s even less of a sex object than, say, Sigourney Weaver in the later Aliens movies.
I think Faye should be exempt from this thread entirely. She intentionally makes herself into a sex object, including advanced cosmetic surgery, to prey on those that are weak to it. The fanservice shots, notably, only occur in the scenes when she is deliberately flaunting herself to try to lull the men (and, occasionally, women) she’s with into letting their guard down. It’s effective, and she makes a successful living as a con artist by turning herself into walking T&A - and she despises herself for doing it. She’s the most psychologically troubled character in the main cast because of it.
It was another scene later in Ninja Scroll that takes it off of my movies to introduce people to anime with. The same woman is unconscious and one of the demons wets a few of his fingers in his mouth and then inserts them inside the woman’s vagina. It was completely gratuitous. Then there was the whole “You have to sleep with him to save him” thing. I like Ninja Scroll but there are a few parts of it that bother me.
Then there’s Mikuru Asahina, in the Haruhi Suzumiya universe. Yes, Haruhi (a girl) dresses up Mikuru (another girl) for fan service and blackmail. However, Mikuru is a time-traveller, sent back in time by her older self to keep an eye on Haruhi. Her older self knows what her younger self will go through, so she undergoes the fan service to serve her own aims – even though it’s not really clear what those aims are.