Barney's version had some pretty solid aging work on display, progressing Paul Giamatti's character over the course of several decades. But how many people have seen the film? How many people liked it?
Then there's The Wolfman, with frankly awesome transformative magic spun by makeup god Rick Baker. People seem to forget that there's a whole lot more than just a hairy Benicio del Toro in this movie, but all manner of illnesses and wound effects that required just as much care and artfulness. Again: how many people have seen the film? How many even remember it? How many want to?
Since we can't rely on any perceived popularity to point us to the winner, we have to fall back on the old most-equals-best philosophy the Academy employs in the craft categories.
Will win: The Wolfman
Runner-up: Barney's Version
Should win: The Wolfman
Should have been nominated: Harry Potter and the Deathly Hallows: Part 1