Speaking for myself, I see Her in that philosophical bucket. It hits with folks who like artsy movies, intellectual movies, culturally introspective movies, etc... It has more in common with Eternal Sunshine than Jurassic Park. The kind of movie nobody says is "bad", but plenty of people say "meh not interested." Some of your comments seem to indicate it's more important to the zeitgeist than most folks would agree with.
"The Best" tend to have real staying power, as opposed to being box office hits. How many science fiction movies to you remember form the 1950s, for example? My mind immediately jumps to 2, then another 2 sort of sneak in the back door when I'm not looking:
"The Day the Earth Stood Still" - Arguably the first anti-nuke movie made in the US. Sure, it has a beautiful girl and a big shiny robot, along with a little action, but it's more about taking a good, long, dispassionate look at ourselves.
"Forbidden Planet" - Another one with action and a big robot, but it's based on Shakespeare's "The Tempest." It covers the nature of man, good and evil, etc..
The others...
"Invasion of the Body Snatchers" - A movie with multiple remakes. Thinly veiled allusions to communism and the Cold War, the nature of being, etc..
"The Thing From Another World" - aka "Invasion of the Carrot Man from Outer Space." A good enough shoot-'em-up SF that it has been remade, twice. More thinly veiled allusion to communism and McCarthyism.
These films are watchedd again and again, debated over, or just plain enjoyed. I don't know that many movies that rely too heavily on special effects, rather than story and character development, will be able to say the same.