Nice post, with a lot of interesting points.
I guess first and foremost I should say that I have not read the book, I've been meaning to, but haven't gotten around to it yet. So obviously I cannot make any comparisons to the book, but that is something I rarely do to any movie that is based on a book. For me, literature and film and two very different beasts and when you adapt one to the other it becomes something very different. No film can do justice to a novel that it is based on, because they are entirely different mediums. For this reason, I often judge movies on their own and try to make no comparisons to books that they are based on, what's the point, you know there are only going to be differences, and if you love one version, these differences only serve to upset. Like you say making a list of differences would be a dissertation, so what's the point.
One thing is that I definately wouldn't refer to David Fincher as your 'typical' Hollywood director...Alien 3 aside, when you look at his films (SE7EN, The Game, and Fight Club) these are hardly mainstream films and definately have a unique style. And he certainly has more of an artistic vision than some directors mulling about in Hollywood. I also think that he put quite a bit of trust in the audience. I certainly don't know any five year olds who would be watching and understanding this movie. As for the Starbucks, he's showing the members of Project Mayhem destroying a corporate coffee house and a symbol of commercialism, when I think of the top three symbols of commercialism in America, Starbucks is one of them, so why wouldn't he use this image, isn't that the point?
The ending...well, again, I haven't read the book, so I guess I'm just going off of what you wrote, though I wouldn't say that Tyler/Jack did not go through a change in the movie...at the end of the movie he finally reaches a balance between Jack/Tyler and is both of them at the same time now and able to choose his actions without relying on the other persona, that's a pretty big change I think. As for the gunshot to the face and killing of Tyler, it's a symbolic gesture, of letting go and accepting responsibility.
As for the visuals, well, seeing as this is a visual medium, and covering a story that has shocking images, it makes sense that we would see shocking images...to me at least. As for the CGI sex scene, I believe it's shown in that fashion to give you the impression that it is a dream, because that is how Jack/Tyler sees it in the morning, when in fact he later realizes it was real and they show a brief clip of him (Norton) having sex with Marla(non CGI). As for the duvet, in film you have to be able to get your message across much quicker than you would in a novel, obviously. The conversation of the duvet is symbolic of just how much unnecassary crap that has been created to serve to the consumers. What is a duvet, it's a blanket, just a blanket. I think this conversation gets this across very well. As for Brad just appearing a chair after a pan, it gets the job done and shows that Tyler can just 'appear.' Do you have a suggestion for another way to show this?
Anyway, I can understand where your coming from and respect your points, but I think your just a little hung up on comparing the movie to the book, which I've found in the film world can only serve to hurt your enjoyment of the two mediums, but that's me.
PEACE
Agalloch