Movies are much too subjective. 12 monkeys had some fine writing, but the editing, direction, and acting are way better in Inception (IMO of of course). Is it an all time great? Not sure, but it's a darn fine movie
If you haven't already I would highly recommend you watch The Pier (La Jetee) which was the inspiration for 12 Monkeys. It has a really beautiful and unique style being composed almost completely of still images which suits the story very well.