Here's one that might surprise some folks: Citizen Kane, the classic 1941 debut feature from Orson Welles. This is a great film, to be sure, but one that has been insanely and consistently overrated by at least one or two generations of critics and scholars. This is not only not the best film of all time, it's also not even Orson Welles's best film--The Magnificent Ambersons and F for Fake, to name two titles, strike me as more substantial and mature achievements.
Citizen Kane is very much a young man's film--with all the hazards and missteps that that might suggest. It's like the dazzling, even gaudy toy that a young genius has devised, showing to the world all the trickery and cleverness that he has up his sleeves. Technically impressive, the story is painfully hackneyed, and some of the often excellent acting occasionally and unfortunately hammy. A masterpiece, but a flawed masterpiece that is rarely discussed as being flawed--therefore, overrated in my book.