Here's a good video essay on the evolving ways Charlie has approached his pet themes throughout his work.

Says Open Culture:

Now acclaimed as a screenwriter and the director of the films Synecdoche, New York and Anomalisa, he brought his penchant for the intersection of the philosophical and surreal even to the first projects he worked on. These include episodes of television shows like Get a Life, the early-1990s sitcom known primarily for its weirdness, and the more subtly askew Ned and Stacey a few years later. But only at the end of the 1990s did Hollywood and its audiences taste Kaufman's writing in its purest form in Being John Malkovich.

Being John Malkovich [...] launched a cinematic exploration of Kaufman's signature themes: control, connection, identity, mortality. That exploration would continue in Kaufman and Jonze's next film, Adaptation, as well as in his collaborations with director Michel Gondry, Human Nature and Eternal Sunshine of the Spotless Mind. "Writing with Honesty," the Channel Criswell video essay above, shows us how Kaufman has approached those themes in the films he has written for other directors as well as for himself. (Source)