The hate for the film seems a bit irrational...
Most of the hate comes from the fact that MNS is playing a character whose work will inspire one to change the world and people associate that with him being egotistical, pretentious, etc. This argument doesn't hold much water considering if a person other than MNS played the character, would the movie have been automatically good? That seems to be the case. People are also unfairly trying to blend the lines between fiction and reality of MNS's character. He is simply playing a character. In no way, shape, or form is he trying to make a statement of how Messiah-like he is. It's a really crappy way to say a film is bad. That's like saying Clint Eastwood is a racist because of his character in Gran Torino. He's simply playing a character who happens to be racist. That doesn't mean he's racist in real life!
Another thing that I found to be a common complaint is that the characters in the film just happen to go along with the whole story without questioning its truthfulness. MNS could have easily solved this problem with using flashy special effects to show that Story was a narf and not some naked girl in someone's shower. For example, in Race to Witch Mountain, the two alien kids had a hard time trying to convince this one character that they are, in fact, aliens. So one of the aliens decided to use telekinesis to move a laptop without touching it, thus convincing the character that they are mystical beings from outer space. But guess what, Lady in the Water is not a film that showcases CGI and effects and implying that the film would have been much more convincing with the use of special effects just shows how little imagination movie audiences have these days. Also, complaining about how people just went along with the idea to save Story is stupid because it was obvious she had an effect on people when they first laid their eyes on her. This was perhaps a substitute for showing special effects to wow the audience.
Other than that, if people stop trying to make a mountain over these two small molehills, I will have no doubt that people would enjoy the film a lot more. Sure, it's a flawed film. Some of the dialogue is a bit clunky and there could have been more of a threat than one "evil" dog preventing Story to go back to her home, but it's a magical film with a beautiful message and a terrific performance by Paul Giamatti. "Every being has a purpose." How can you guys seriously hate this film with such an uplifting message?