JJ seems to go for the superlative effects possible for a genre (such as Alias, a Bondian show with peerless action visuals), whereas Del Toro seems to go for effects that you won't find elsewhere (Biblical angel from Hellboy 2, underwater nuclear explosion from Pacific Rim, etc.) Also, based on the two films I've seen of theirs this year (Star Trek 2 and Pacific Rim), I would say Del Toro's films have more originality and substance to them, and targets more specific audiences, whereas J.J. just wants to entertain the general audience and please as much people as possible.
Just some comparisons. Both are awesome directors though, so obvious stalemate.
JJ knows his craft yet so does Toro.
Yet Toro has the balls to enter horror/comic fiction as a director.
He wins in Horror but his attempts in comicbook/sci fi related ventures fall flat at times. Due to his non Hollywood style in directing.
Both are visionaries and personally del Toro edges out due to personal taste.
Guillermo takes heavier risks and stares fantasy in the face and pushes forward.
These two shouldn't be weighed against but Guillermo has made films that I can always go back and watch again for they are simply classics.