I've read the manga and seen the anime, and other than common names, it almost seems they are completely different animals at times.
The feature-length anime essentially explores the significance of Self and Individuality, and wonders if robots with implanted human wetware can have "souls." It also explores whether an A.I. can have a desire for "procreation" or a survival instinct. The Puppetmaster A.I. is the mirror against which the characters and viewer have to examine themselves. The movie is much deeper than the anime on a personal, human level... it asks the viewer who, and what, they really are.
The manga's themes are essentially about the familiar foibles of man, ie, his basic sins, in a world where the network ties everything together so pervasively. It's a cop show on web/droid steroids. The main characters don't spend that much time wondering about their essential natures, they're basically just trying to stop the various national or international information theft plots of the day (as the manga, and the anime for that matter, asserts that information is the only thing worth stealing). The subplot involving the Puppetmaster is almost lost amidst the static, which the manga suggests will be commonplace as technology and complexity eventually overwhelm humanity. The manga suggests that who you are is irrelevant, that you will be assimilated, and resistance is futile.