The most striking difference between both works is that the fate of the protagonist fighting the system. Winston loses, while Neo wins. Winston struggles to fight against Big Brother. He launches actions of resistance on different levels. In the end, though, the power of Big Brother is stronger than what he can offer. His experience in Room 101 causes him to abandon his theoretical foundations, betray himself and Julia, and thus return to Oceania as someone who is "plugged in" to what Big Brother wants.
Neo does not follow this same trajectory. While he might not be willing to accept his role as "the one," he understands that his loyalty to Morpheus and to the function of Zion compel him to follow through on his resistance. When Neo must face a moment of truth, similar in some respects to Winston, Neo accepts what he has to do. He frees Morpheus from the Agents and himself embraces his purpose as "the one" when he defeats Agent Smith. The ending of the film sees Neo calling out to more people to join the movement against the matrix, something that Winston is incapable of doing.
The social backgrounds of each work are similar. Winston and Neo face worlds in which a centralized force of power ensures conformity and control through its being. Big Brother and the Matrix demand social control and its enforcement becomes the reason for authority's being. Authority is seen as a force to control and suppress resistance. Winston and Neo recognize this early on in their narratives and much of their characterizations is rooted in this relationship between the individual and the authority structure that envelops them.