Chrono Trigger has all the elements done right- 10/10 music, 10/10 art style, RPG and battle systems that were innovative for the time and are still fun to play today.
But I think what sets the game apart as a timeless classic, a masterpiece, is its deep themes of existentialism. Marle has has a fake persona and a mistaken identity, yet we can still see her real self. Crono, as an avatar for the player, is sentenced to death and spared in the last moments. Robo, after being freed from his original programming, asks "Is this what it is like... to die?"
And that's all just in the first act.
The ideas of Sartre, of Nietzsche, and perhaps most of all "Being and Time" by Heidegger were presented in a way that my 10-year-old self could comprehend and enjoy. But it's not dumbed down for children, my 30-year-old self can still find deep meaning in the narrative and themes.