It isn't anybodies fault, or won't be if it is addressed.
Firstly, 8 teams playing each other 3 times means that a team that does not have to entertain and can sustain a draw or rely on a smash and grab has a huge advantage. They have seen all the tapes, they know who can do what.
Secondly, I am afraid it is the refs.
Refs know all the players. They know what to expect from them, so when a known diver is fouled, he dived and gets a yellow card.
Refs know all the grounds and crowds. So when a crowd complains about a decision, the ref can rest easy, the FFA will back him. He does not have to worry about entertaining the crowd. And at most grounds he is protected from poor decisions by an agreement that has the big screen blanked out on contentious decisions - cutting down the reaction of the crowd.
As a result of these factors, the ref tends to a psychological position where he biases against the home team. He will discount the home crowd and their groans and shouts and assume innocence and favour the away team. It happens every week, no matter how good the ref.
This is so wrong. This does not happen in 22 team competitions. In bigger competitions, the refs don't have personal relationship with the players, they don't have to worry about what they know of player who has fouled or is fouled (even the FFA is susceptible to this look at the way they suspended Tiatto post match and then ignored worse fouls for the rest of season). The lines-people get more experience in bigger competitions and therefore they make better offside decisions. And the leagues can afford for the refs to be full time - review their performance each week and train.
It is wrong because often the crowd is right. In the Roar v Sydney match Renaud and McFlynn's mission was clear, take it in turns to foul Minniecon, Zullo and McKay to slow them down or take them out. They succeeded, and the ref allowed it. Similar tackles by home teams, even by Sydney, had been met with yellow and even red cards in earlier games.
When the home team gets punishment and the away team gets away scot free, crowds get cynical and ultimately stay away. This happened for Wellington with Ross Aloisi getting sent off for a tackle at the level that Ufuk Talay had had ignored.
But worst of all is when the refs anti-crowd psychological self protections lead to the dismissal of clear penalties. Like Kevin Muscat's, as described by the Courier Mail (14 Jan 2008 p58), 'blatant hand ball' was ignored in round 19 Roar v Victory, and last night when Ufuk Talay's hand ball and Renaud last man trip on Minniecon were both ignored. All these events made the news, the game provided the video evidence and the refs' poor, anti crowd decision making put the games into disrepute.
How to address this? Video replays. More refs who don't know the teams (guests). Replays of all major events at the ground.