According to Nintendo UK, the version of Animal Crossing shown for 3DS was primarily to show how it might look on the handheld.
Like a handful of titles demonstrated on the new handheld, Animal Crossing was shown as an example of that sort of game and visual quality, rather than screenshots and footage from the actual game in development.
Speaking to 3DSBuzz, James Honeywell, Nintendo UK’s head of marketing, mentioned that "…the demo was shown at E3 to showcase how an Animal Crossing game could and might look running on 3DS."
Rest assured though, the game is on Nintendo's release lists and has come up various times since E3, but the final version could, though unlikely, look completely different.
What would you like to see from a new Animal Crossing game for 3DS?