One of the most dominant themes in the film centers on the nature of reality. Neo, and by extension the viewer, must assess "What is real?" This becomes one of the basic themes that drives the film because throughout it, Neo has to continually ask himself what defines reality for himself, for others around him, for the machines, and for Zion. In a way, another theme of the movie is the how reality comes to define the self. As Thomas Anderson, reality is defined as adherence to the rules and thereby unknowingly following the repressive demands of the matrix. It is only as Neo does he understand that his real sense of self is one in which he must break out of the construction of the matrix and "unplug" others in the process. This helps establish another one of the themes in terms of free will and control. The characters in the film must choose whether or not to accept the construct and design of the matrix, whereby free will and the idea of choice is eliminated, or return to the insecure future and status of Zion, where choice and freedom are realized. Cypher, for example, makes the choice to remain in the world of social control, while others make the conscious decision to embrace the world of freedom, regardless of its consequences and cost. In this, one sees basic themes played out in the plot development of The Matrix.
Thank you for your answer akannan, but I want more ideas that focus on the fact that the film exihibits themes of dystopia and how the characters are prone to thinking that the world that they live in is perfect, but as a viewer, we are able to see that there are aspects in the films that are of dystopian nature.