I wouldn't consider Empire OR Khan to be in the top five best sci-fi films ever made, let alone the top two. What about 2001? Or Blade Runner? Children of Men? Moon? Planet of the Apes? The Day the Earth Stood Still? Invasion of the Body Snatchers? Abre los ojos? Alien? The Road?
I could go on, but I'll stop. My point is, every one of those films is (in my mind) superior to both Empire and Wrath of Khan, at least as science fiction.