Many reviews were quite negative and a lot of people seemed to not understand the story. I thought it was terrific - a finely worked piece of art. Here is the explanation of the story for those who didn't get it:
Six (James Caviezel) in the real world was determined to figure out what he had been working on for the secret mega-corp headed by the Two character (Ian McKellen) - it turns out Two is an eccentric rich fellow who wants to fix broken people and constructed a Matrix-like Village in which these peoples' minds could live and prosper within the confines of the construct and its rules. Another person held the construct in their mind - the wife at the beginning and the doctor/love interest later ... and this person had to be asleep or the construct began to unravel (the holes). The whole point of the story was that Two wanted to replace himself and he cultivated Six because of his strong moral compass. The trials and tribulations Six went through were to test his mettle and by the end he proved himself and Two was able to move on. Six indeed became a prisoner, but a willing prisoner - bound by love.