Macbeth is the greater play, I think. It's much more widely staged, taught, and reviewed by critics. It generates hundreds of pages of criticism not only in literature and drama, but also in history, psychology, philosophy, and the social sciences.
Macbeth is much more modern and humanistic. Faustus seems stuck in the mythical, supernatural, and Medieval.
For whatever it's worth, in Daniel S. Burt's The Drama 100 : a Ranking of the Greatest Plays of All-time, Macbeth was ranked #5, and Doctor Faustus was unranked. That shows you the disparity.