BTW, how many posters here knew The Departed was based on the Hong Kong trilogy 'Internal Affairs'?
If they didn't know, they could have just watched the broadcast. They said it multiple times. The screenwriter even thanked the original movie.
Essentially, the Academy gave Scorsese the Best Director Oscar as a makeup of him not winning for Goodfellas and Raging Bull 16 and 26 years ago.
This is really common and a lot of people don't really notice it. Sometimes it's to make up for someone being overlooked after a long career. Paul Newman's win for Color of Money (one of his least interesting films) falls into this category. James Coburn won several years ago the same way. And obviously Al Pacino deserved it way before Scent of a Woman. You could make an argument for Henry Fonda in On Golden Pond and Julia Roberts in Erin Brockovitch.
Then there are others that make up for a very recent Oscar snub. Judi Dench should have won for Mrs. Brown, but instead won for her cameo in Shakespeare in Love. Jeremy Irons should have won for Dead Ringers, but got it for Reversal of Fortune instead. Russell Crowe won for Gladiator, but was far more worthy in The Insider. And I think Elizabeth Taylor won for Butterfield 8 to make up for several better performances that she had been nominated before.
I think it's a side effect of the craziness of trying to narrow such varying performances and movies down to one winner.