AFL have had major issues including the Essendon peptide dramas and the massive cocaine use by it's players. No sport is without it's problems. The NRL gets picked on by the media because of it's working class roots and the fact that it is an easy target.
The AFL is run better because it has the resources to ensure the best people are running the game. It doesn't have a State of Origin nor an international scene but will always easily be the #1 footy code in Oz because of it's broad appeal and professionalism, an advanced junior program, very wealthy clubs and backers and a sound template for the future.
RL has always been full of idiots from top to bottom who are simply in it for themselves eg. Cam Smith and Craig Bellamy and whilst IMO is a much more mouth watering product, it will never approach the popularity of the AFL. The Lion's attendance figures have been better than the Broncos on a couple occasions this year. That would never ever happen in Melbourne.