Looking back, I personally think Babel should've won because The Departed was simply near-perfect execution of a good Cops and Robbers movie, while Babel was an innovative picture that made a sweeping statement.
I think in general, genre pictures that are honored by the academy (My Fair Lady, Broadway Melody of 1929, Great Zigfield for musicals, Cimarron for Westerns, and French Connection for cops movies) can get dated pretty quickly. Whereas epics and films with sweeping statements or films that touch on relevant themes. There are obviously exceptions to this rule (i.e. The Godfather was the hallmark of gangster films and American in Paris, West Side Story and Sound of Music are among the best remembered musicals) but generally films that revolutionize and bend the genre like High Noon, McCabe and Mrs Miller, and The Searchers for Westerns or Singing in the Rain for musicals or Little Cesar or pretty much the entirety of film noir don't get recognized in their day and only get appreciated later in retrospect.
So in essence what I'm saying is that the genre pictures that really revolutionize the genre and find an innovative method of redefining it, generally don't get honored right then and there because it takes time to realize the brilliance of it. You need films to follow the particular trend that a revolutionary picture like High Noon is starting before you see how significant of a film it is. This is not neccessarily true: sometimes films that are innovative like West Side Story or the Godfather get honored, but these examples are rare and if a genre film wins, the academy usually will honor a film that executes the existing conventions well. The Departed is in no way revolutionary, but it is an excellent execution of a gangster film. It is also a personal triumph within the Martin Scorsesee canon, in that he was able to return to form. He was able to leave the grandiose ambitions with which he brought to the Aviator and Gangs of New York behind and buckle down to make a solid gangster film. However, the best picture award he received reflected more of a decision to avoid a director/picture split than it did a convincing vote for a best picture. While I concede it was a close race, I personally think that Babel was that epic thematically relevant film which was well-made and spoke to the problems facing the present.