The Matrix was fairly unusual.
Unusual, but I dunno about new. New to film, maybe, but virtual reality worlds is old as computers in science fiction.
Wall-E I thought was unique.
Unique in its celebration of authoritarian decision-making in a children's film, but built on what may be the oldest tropes in the book. The theme of a ruined Earth and a subsequent interstellar exodus has been explored in countless fictions, and I can trace the film's central notion, that the twin advances of technology and automation are a great moral danger to humanity, to at least as far back as The Machine Stops (1909). Indeed, even the visual aspect of the fat Americans of the future was excessively similar to "Blobs!", the Harvey Kurtzman/Wally Wood comic adaptation of E.M. Forster's classic.
It's a marginal opinion, but as far as I'm concerned Wall-E was a tremendously unoriginal film, with an extremely questionable and undemocratic bent to its moral.
How about Idiocracy? Dumbing down of society to the point where water is just something in a toilet, not something people drink and they can't figure out why plants are flourishing on the future "gatorade" type drink.
Sort of like Planet of the Apes, but I'll give it credit for being a very original take on the future (if obviously a crock, sociobiologically speaking) and a good, allegorical cautionary tale, as well as a great comedy.
And the Incredibles. Super heros forced to retire because of insurance liability concerns.
Very similar to the premise of Watchmen (forced to retire because of social backlash against vigilitanism), although I think it was probably new there.
As for 2001, it probably wasn't new (its techniques were new, to be sure!), but I suspect there had been stories of apotheosis-via-alien before, although I might be wrong.
And Dark City--I'm sure that Dark City wasn't the first time the "world" turned out to be an alien spaceship or some other camouflaged environment, for the benefit of human prisoners or zoo exhibits.
I can't think of any film sci-fi off the top of my head with any really new ideas.
Edit: Clearly, I wasn't thinking hard enough! The Truman Show, Gattaca, and Simone--Andrew Niccol's works, although suffering from a slight to severe disconnect from how the real world actually works (corporations adopting a child to basically raise him as a slave in Truman, pointless anti-qualified-normal bigotry in Gattaca, Frasier-esque comedy of errors in Simone) have usually been extremely original and thought-provoking, and reflective if not exhaustively descriptive of social trends. Dude's probably the smartest, best science fiction writer in film history. Okay, it's not an especially high bar...
I wonder if Vonnegut's Player Piano was the first work to anticipate the economic dislocations that would occur after complete automation in a capitalist society? Probably not, although it's the first example I can point to. Here's a contender, though--Stranger in a Strange Land might be the first work to have an alien messiah come down and tell us what we need is to fuck more often and more generally.
(Apropos of nothing, does that book have a completely worthless last fifty to a hundred pages or what? They have the feel of an inferior sequel instead of an integral part of the narrative. I understand I have the restored version, and I wonder where the original publishers' edit ended--there is a pitch-perfect note to end on well before the book actually terminates, where Michael discovers why we laugh. Everything past that is unnecessary, occupied primarily with the mundane, boring details of Michael building his religion. He's Space Jesus, I get it, Robert. Indeed, this has effects beyond the immediate book--the awkward, pointless last eighth of Stranger has kept me from continuing to read The Moon is a Harsh Mistress past the part where the Loonies actually win. I'm not sure I want to spend time with the mundane, boring details of building Space Libertarianism.)
Oh yeah, that's right: Marvel comics. Darth Vader is an obvious steal from Doctor Doom which was a steal from The Man in the Iron Mask. Vader also had a family structure suspiciously similar to Magneto...
It's all variations on a theme-see below.
