The way I see it, the main advantages Scrafty has over its most similar betheren (Conkeldurr) is that it adds that Dark typing into the mix, which allows it laugh at the Ghost and Psychic types that usually give Conk trouble (though Conk isn't a slouch at taking those out itself, with Payback at its disposal). It also has more versatility, allowing to fill other niches as well. I think the reason why its usage is down though is simply that for most teams another Pokemon usually fills the role better. Dragon Dance Scrafty, while no doubt dangerous, is far from the most dangerous user of the move, with Dragonite, Salamence and Gyarados being the first choice for most teams. Bulk Up Scrafty faces intense competition from Conkeldurr and Breloom, and it usually loses out to either one due simply to the lack of power it has, meaning defensive Pokemon can frequently screw it over as it tries to set up.
Basically, it's a niche Pokemon. It has enough to set it apart from the competition, but what sets it apart isn't usually what's needed on most teams. As such, it's relegated to the bottom of OU. That's my take on it anyway, I've never used Scrafty, though I HAVE used the alternatives.