I prefer the relationship between them in the movies. It's like they're perfect strike-team partners - she's the point, while he backs her up. And there's an unspoken bond between them....he cares for her (putting his coat/vest on her), and she cares for him, saying (at the end of Innocence) that whenever he logs into the Internet she'll be right there with him. It's not affectionate or romantic, but it's as close to a loving relationship these 2 can ever have, given their respectives personalities (& remember, in the movie, Kusanagi isn't human any more, she's something greater & grander after merging with the Puppeteer...)