It would be great to see the largest training agency in the world come up with a ratings system that would tell their divers whether operators were following standard safety procedures and properly equipped to deal with the hazards their divers might face. Unfortunately, I don't think working with PADI will get much of anywhere for the Bali operators (or any others), since PADI's "5-star" rating for dive centers apparently has very little to do with quality and is mostly based on how many PADI certifications and training materials they sell.
Ok, so say PADI/SSI goes out and inspects these places, everyone gets advanced warning and cleans up their act. A few weeks later things start to slip by the wayside again. None of the training agencies have the resources to be monitoring these people 100% of the time. I don't think getting someone out once a year or so is really going to help.
As someone else indicated, a good percentage of the dive ops in Bali have no affiliation with the training agencies anyway and will just continue on as they have been. The non-affiliated ops are catering to the backpacker/budget traveller market where cost is often more important than safety to their clients. I gave a friend of mine (newly certified - had no dives other than the OW cert dives) a recommendation for a dive op that I've used in Bali a few times who I've had good experience with, and they balked at paying the extra $30 for the day trip compared to another (IMO) less reputable operator.