As a series, Appleseed differs by focusing primarily on world politics and counterrorist operations, whereas GITS uses these premises as a backdrop, but attempts to go deeper philosophically by questioning human existence. Most critics seem to prefer the deeper approach of GITS, and pass off Appleseed's recurrent plots as purely action-oriented and shallow; in reality, this is a mistake.
The manga is sociologically quite deep as well, almost to the point of confusing its readers, which is probably why the audience is more polarized as to either loving or hating the original series. The socio-ethical question posed in Appleseed, similar to GITS, revolves around the mechanization of humans through cyberization, but adds the bigger issue of producing genetically engineered human superiors, called the Bioroids. Intentionally, though, these hot-button controversies take back seat as more imminent threat of destruction is posed through war, drugs, and terrorism. The timeframe depicted is nearly a century later than GITS, and the pace is far more harried as the world's end draws nearer.
Some have said that the animes which were later produced struggled to convey this substance effectively, and lead to the mistaken opinions regarding the series' real nature. That's not to say the movies are bad, for they were quiet smash hits in their own regard—more just that they interpret the subject matter quite differently than they could have, and leave out a great deal of content. That said, Appleseed XIII, a new attempt to shed light on Shirow Masamune's original stories, seems like it will finally give the series the Ghost in the Shell treatment (and hopefully reception) it deserves.
--DID YOU KNOW? There was already an Appleseed TV series planned for 2008, but it was canceled due to budget cuts and other disputes.
GETTING TO KNOW THE SERIES