Dark City and The Thirteenth Floor are a few of my top sci-fi movies of all time. Both have themes that echo the Matrix, but done in a much more subtle and thought provoking way IMHO.
It's a shame The Thirteenth Floor came out the same year as the Matrix...
Yes yes!! these are two of my favourite all time movies. Kiefer Sutherland acting in Dark City is amazing. Those are two movies I can re-watch several times without getting tired of them.
and all the Verhoeven movies 1985-1997
https://en.wikipedia.org/wiki/Paul_Verhoeven
Not based on P.K. Dick works but heavily (and beatifully) inspired by them I'd also mention "Dark City" directed by Alex Proyas (The Crow, I Robot)
https://en.wikipedia.org/wiki/Dark_City_(1998_film)