LGBT Fanbase: Ghost in the Shell meditates a lot on the nature of personal identity, one's "ghost" in the series, and how it often doesn't match up with physical appearance, one's "shell"—which is readily changeable through cybernetics. As a result, it tends to resonate with genderqueer readers in particular.
Trans Audience Interpretation: The Major is presented very much as The Lad-ette and in the original manga is canonically bisexual, and in at least three continuities (original comics, Stand Alone Complex, and film), the name "Motoko Kusanagi" itself is only an assumed identity. In several continuities she also eventually sheds her feminine-presenting physical form altogether and seamlessly switches between masculine and feminine prosthetic bodies afterwards as needed. Thus, she is sometimes interpreted as being trans or non-binary.
The lesbian sex scene in the original manga. Comes out of nowhere, is never brought up again in that book. And was even edited out by the North American release.
Man/Machine Interface had a sex scene involving a female African soldier getting gang-banged by 3 other soldiers. Shirow admitted to removing it from the North American release, just like the above, because it really added nothing to the story.
Designated Hero: While she's on the job, the Major is not a nice lady; at times, she seems to approach being a Sociopathic Hero. For example, in Section 9's first mission to determine if they would even be approved as an organization, Motoko ends up saving the lives of boys who were working in hellish totalitarian conditions and barely being fed. When they ask if she was here to help them, she told them that they have to make their own lives and not rely on hand-outs. Ouch.
Fetish Retardant: A sizable faction of the fans maintains that Man/Machine Interface is unreadable because of this. The other faction maintains it is only readable because of that.
Hilarious in Hindsight: The Puppet Master is a powerful artificial intelligence program designed for mass domestic surveillance and political manipulation developed by the Ministry of Foreign Affairs and Section 9's rival, Section 6. When the program becomes sentient, it then tries to defect, with Section 6 desperate to recover it for fear that the revelation of its existence would cause massive political fallout. Twenty years later, and the scandal revolving around the NSA's warrantless domestic surveillance programs and the information leak of the program by NSA contractor Edward Snowden almost takes it out of the realm of fiction.
Misblamed: Some have claimed the lesbian sex scene's removal was due to overzealous localizers, when in fact, the original author himself opted to have those pages removed. Whether that makes things better or worse is still a source of debate.
Once Original, Now Common: The franchise was a huge influence on The Matrix and on the cyberpunk genre as a whole. However, newcomers to the franchise likely saw Matrix first, and most of the themes of identity and people and machines were already covered there, and so many people wondered what all the fuss was about. This was even cited a major reason why the remake failed to attract Western audiences. Honest Trailers put it thusly:
Epic Voice Guy: "...the source material was so influential that now it feels like it's copying the films that it inspired."
Older Than They Think: Ghost in the Shell has an unique relationship with Angel Cop, another Japanese cyberpunk franchise protagonized by a wild, blue-haired female cyber-cop. The original GitS manga kicked off only one month before the promotional AC manga did, while the AC OVA series finished a year before GitS got its first animated adaptation, so there's a fair possibility that the two franchises actually influenced each other instead of one being just a Whole-Plot Reference to the other as it is often believed.
Sequelitis: It's extremely easy to find fans of the original manga. It's much harder to find fans of Human Error Processor or Man/Machine Interface. The latter are frequently derided for their cheaper artwork, loads of Technobabble, and general Mind Screw.
Signature Scene: The Major jumping from a skyscraper, shooting someone through a window and camouflaging as she falls to the ground in her first story. It has become a mainstay of the franchise's visual style with the 1995 movie, Stand Alone Complex, Arise, the Scarlett Johansson movie, and 2045 using it.
Woolseyism: The English title is the subtitle of the original work. The actual Japanese title, Kokaku Kidoutai, translates to "Mobile Armored Tank Police". (Shirow Masamune mentions in the preface to Man/Machine Interface that the Japanese title is a huge misnomer for M/MI, because the story is no longer about the police, nor does the protagonist ride in an armored tank anymore. He considered changing it, but... nah.)
Video Game
Broken Base: The fact that the game is basically an arcade shooter focused on fast-paced action with none of the complex philosophical stuff the 1995 movie had. Some fans are irritaded because for them it means that it’s a poor adaptation not worthy of its positive reception but others will point out that, since it owes a lot more to the original manga, which was much more focused on action and it uses the Shirow’s more goofier artstyle and lighthearted character interactions, that it’s actually more faithful and fitting than they realize.
Complete Monster: Zebra 27 is a mercenary who once carved a path of destruction through Africa before being hired to lead the Human Liberation Front. Leading terrorist strikes against New Port City that leave a hundred people dead or wounded, Zebra further sics mecha tanks onto populated civilian centers to distract Section 9 from capturing him. Zebra's ultimate goal is to take a nuclear reactor hostage to extort a fortune from the government, threatening to blow up the reactor and "make Chernobyl look like a picnic" if his demands aren't met.
Just Here for Godzilla: Some fans are interested in the game because it features animation with an artstyle much closer to the original manga and because it features the original English voice cast from the 1995 movie reprising their roles, especially notable as this was the last time Mimi Woods would voice Motoko before retiring and falling from the public eye in the early 2000s.
No Problem with Licensed Games: The tie-in game made for the PlayStation is surprisingly well-received by fans, with a surprisingly high score - 8/10 - on IGN. The general consensus is that it's an above-average Third-Person Shooter where the player can kick plenty of ass in a Fuchikoma all over the place, and that it has a Wall Crawl gimmick that the player can handily use to scale walls, ceilings, and ambush enemies from above or dodge attacks. It was in fact listed by Game Informer some fifteen years after it's release as one of the best manga and anime-based games.
That One Boss: "Encounter in the Darkness" has an agile, lightning-fast Spider TankKing Mook who has a cloaking device. It fires projectile attacks almost non-stop, can absorb a ton of damage, have a habit of staying out of the Tachikoma's range and... have we mentioned it's invisible most of the fight?
Visual Effects of Awesome: The opening cinematic. It’s a masterful blend of traditional animation and CGI, and, rather unusally, it was animated at a slighty higher framerate than most anime productions at the time, resulting in some extremely fluid movement.
The cinematics are basically movie-quality and seeing Shirow’s artstyle animated with so much detail is nothing short of eye-candy. It really makes you wish there was a whole movie animated like that.
The in-game graphics are no slouches, either, as they still look really good nowadays for PS1 standards. At times, the textures and model work look like from an early PS2 game.
and the information leak of the program by NSA contractor Edward Snowden almost takes it out of the realm of fiction.