The Matrix was influenced not only by Ghost in the Shell. Action aesthetic of The Matrix was influenced by anime in general, it's just Ghost in the Shell is the most recognizable. I think the only real influence on the world of The Matrix - link cables.
Yep, I read that article about The Invisibles long time ago, but forgot about it. I never read the actual series. Given the amount of similarities, it really felt unfair that Wachowskis never mentioned it (as far as I know). Cameron had to insert the acknowledgment message in The Terminator credits, but I think it happened after some legal battles with Harlan Ellison. It looks like Grant Morrison decided not to bother.
Maybe that's the reason why Wachowskis never made a great film after The Matrix - they just never encountered a great source to pick from after that.
Anyway, yeah, I personally don't consider The Matrix to be a western adaptation of Ghost in the Shell.