Dude, the first movie was based on the last story arc of the original comic series IIRC.
It's no secret that Shirow cannot write a clear and understandable story. It's all techno masturbation for him. Go read GitS, Orion, and GitS2. You'll see the man is all about drawing titties and machinery, and the "story" bits are his latest thesis on technology theory.
I've got friends that read gobs of hardcore Sci-Fi that can't even stomach Shirow's "writing".
GitS the animated movie was enjoyable, but aside from a vague connection to the last story arc of the first series, bore no real relation to Shirow's work.
I'm just guessing you're not all that familiar with Shirow's body of work, outside of the horrid animated adaptations. Once you see his natural knack for drawing a nice oiled up rack, you'll agree that he's just there for eye candy.
Quality anime?

Do yourself a favor and rent
Grave of the Fireflies and, or
Barefoot Gen.
I also don't comprehend the rationalization that X Adaptation based off of Y Product should be given free license to totally fuck up the appreciation of Y Product. After all Product X is riding piggyback on the success of Product Y. If you're not going to please the fans, then you're just making another shitty licensed movie.
Here's a novel idea. Instead of taking a well known property and turning it on it's ear because you have your "own creative voice", but not a single original idea in your head, you just make an seperate product and sell it on the merit of it's qualities?
Na razie,
G.A