I mean, even 3-6 themselves admitted that they didn't think that they would win. What do I see this as? I personally see this as the Oscars taking note of the effect and prominence of hip-hop/rap in present time.
Far too long, mainstream (the older audience generally) has wanted to sweep it under the rug and treat it as if it doesn't exist, but how can they now? Now about the Oscar...Scorsese is one of the greats as far as directors go, no contest there, but when you have one of the greats up for nomination, it's a sure bet that you're going to have more than one going up against each other.
Best director is a big category, right up there with best actor/actress, best picture. You can watch a commercial for the DVD of the movie and hear "best director", "best actor", "best picture" all day long. Not likely you're going to hear "best soundtrack song" unless it's a documentary of a musician like Tupac Resurrection or even Walk The Line.
Best song/soundtrack is on a much smaller scale, so it's easy to let that go to a "mediocre rap group". Usually, the song that wins, you've never heard of the people who made it. Hell, truth be known, I had to take a double take on the screen and think "whoa...that IS three six mafia...cool". And you know 3-6 is going to floss that Oscar win and put it in some of their lyrics.