Matrix 1 is timeless to me. a Top sci-fi of all time list. Everything fits well. Us vs. Them, the chosen hero in a new world (still follows the hero's journey motif in cinema). We are with the Hero and its not just about kicking butt as since Neo may be the One he is learning about the world just as much as we are. Sci-Fi is the movie genre that is the most philosophical and this is no exception because the hair raising question is the entire film... (what is real, is this real life?). It was released at a time of internet infancy where as we didn't know what to expect with this new technology that makes information gathering limitless and scare people by simply going to AOL and typing out lyrics to the song that's stuck in your head but forgot the name to.
They created a new enemy for a new generation (those sentinels or Agent Smith or whatever). And its something that we created. The best sci-fi's have always been those that the enemy we created, HAL in 2001 or replicants in Blade Runner. We(humans) deem ourselves intelligence as a source of reasoning for power and want to take down anything above us. The Borg (assimilating AI) in Star Trek Lore and Star Trek:First Contact movie come to mind as well.
It also was a Sci-Fi that changed the cinema game with its special and visual effects and that always leaves a mark on the world.
Matrix 2 drew on those factors for a bit but couldn't carry the movie to positive recognition and #3 was one giant action sequence brought on by #2. Throw those out and keep Matrix 1 and I'm good. 6.9/8