You can almost pinpoint the moment where the writers/producers said, "We need to make this movie more family friendly--throw in some poop jokes and stuff." Which is a real shame because there's a lot of interesting stuff in this tonal mess of a film--genocide! horseshit joke! themes of brotherhood! wacky Johnny Depp!
If you list all the famous actors, famous directors, and famous writers that you know, you'll see that the first two lists probably dwarf the third list. (Or as 30 Rock put it, announcing a Janis Joplin biopic: "starring Julia Roberts, directed by Martin Scorsese, and written by the best screenwriter in the world, whoever that is.") So I don't want to lay all the faults of this movie on the screenwriters, Ted Elliot and Terry Rossio (whose script apparently leaned more towards the supernatural) and Justin Haythe. Some of the problems are clearly in the production. For instance, the casting of Johnny Depp to play a wacky Native American, whose wackiness is not too dissimilar from Jack Sparrow's from the Pirates of the Caribbean. (Actually, there's one moment where Tonto boards one train from another that seems straight out of Pirates in its images.)
At the same time, I don't want to let the writers here off the hook... and yet, while watching the film, I could see that a great deal of craft and thought went into the bones of the story. For instance, protagonist/antagonist mirroring: Dan Reid is a law-minded civilizer from the East. He's back from law school to make the West a civilized place. And Tonto is a half-mad wild-man who operates according to his own symbolic rules of contract that have nothing to do with Eastern/governmental laws. On the other side, the two villains--whose names I have to look up, which surely is a problem--are Latham Cole, the would-be railroad tycoon who can quote Locke as easily as Dan Reid does; and Butch Cavendish, the wild outlaw who operates according to his own rules, including eating the hearts/livers of his enemy. (Shades of Liver-Eating Johnson there.) And just as Dutch's outlawry secretly hides a contractual/brother relationship with the railroad tycoon and the railroad tycoon's civilized exterior hides an outlaw core; so Dan Reid's journey here is to become a little wild while maintaining the urge towards justice and law.
Similarly, the silver that is stolen from the Indian river at the beginning of the story (not the movie, but the story) is returned to a river at the end of the movie. And the theme of history is continually played with, from the emphasis on pocket watches to the continued talk about heading towards the future. (Actually, it could be argued that this theme is hit a little too hard.)
So with all this care and craft, why did this film misfire? I think it's partly the tone/mood, which can never quite settle on one thing, both visually and emotionally. And aren't those the same things in a film? I mean, the movie starts with a dark view of a carnival, which has a Gore Verbinski-esque shadowyness; but then we have the wide-open bright spaces of the Western desert. And the dark mines. And dark spaces in trains. And bright mountain-tops. And night-time meetings with dancing bonfires. I'm not arguing that your film needs to be all day-time or all night-time scenes; but the see-sawing between light and dark is matched by a similar see-sawing in the film, from wacky Helena Bonham Carter as madam with a fake leg that is also a gun, to scenes of gatling guns mowing down Native Americans. It's hard to yee-haw after a scene like that.