You make some very valid points. I think the fundamental reason why "Ghost in the Shell" failed at the box office is because no one had ever heard of the original anime film except for hardcore scifi geeks like us. This is essentially the same thing that happened to "John Carter".
No one except us geeks heard about Deadpool and Guardians of the Galaxy before they released, but they still became hits.
GitS is simply a slow moving, thought provoking action anime, now an action movie with little more to say.
John Carter's problem was marketing. Would it have done better if it was called "John Carter of Mars"?