Main flaw?
My impression of this movie is that it was just so ungrounded in the rules of human limitation and reality that the audience stop caring.
Stories need rules, so that people are challenged, and there's some semblance of predictability from individual and human nature. In this movie Samantha is like the Almighty, able to control Jack's thoughts and behavior and create events and reverse time. That just seems to make everything pointless.
If Sherlock Holmes not only has unfailing psychic powers, but can also change reality and human actions, and cause whomever he wants to have been the perpetrator, and can create clues for it all, then a Sherlock Holmes mystery story wouldn't be very meaningful, would it.
Moral: Stories, like games, need rules.
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