Bell's theorem rests on two main assumptions: locality and independence. Locality has its basis in relativity and it seem to be a property of all known physical theories accepted today (General relativity and the quantum field theory).
The independence assumption (also known as "freedom", "free-will", "no-conspiracy") implies that the hidden variables and the measurement settings are independent variables. This seems intuitively appealing, but is there any reason to accept this assumption?
The modern theories I mentioned above are field theories. In such theories the state of a subsystem is not independent of the state of the entire system. Stars in a galaxy do not move independently of other stars, charged particles do not move independently of other charges even if the distance separating them is large. But the source of the entangled particles and the detectors are nothing but such subsystems of the whole experimental setup. They are nothing more than large groups of charged particles (electrons and nuclei/quarks). So, it seems to me, that the independence assumption is in fact contradicted, not supported by the mainstream physical theories.