How about 'Dark City' (1998) (my favorite "modern" movie)? In its own way it's also philosophical and mysterious, and if you're someone (like me) who despises the old saying "absolute power corrupts absolutely" then this is a great movie to watch. Plus, it's a perfect balance of many different movie genres (noir, SF, mystery, horror, drama, romance, fantasy, action and with a few comedic touches thrown in as well) and also manages to avoid many common movie clichés (both of which impress me a helluvalot). Give this one a try. Definitely a "thinking-person's" movie.
Oops! Okay, then how about my favorite all-time movie? The original 1937 version of 'Lost Horizon'? Very philosophical. Also, a little-known movie with a similar "sense-of-wonder" aura: 'Green Mansions' from 1959. Somewhat more of a romance than 'LH' but still great.
just got back from watching Arrival and it tried to be like alot of the films mentioned here. Can't say i was that impressed but you might like it. When i was watching it Solaris/Contact/Independence Day/Mr Nobody & The Fountain all came to mind.
Ps - Great thread btw. The Fountain is my favourite film of all time, constsantly on the look out for similar films.