Seanog,
I  think the organizational structure you described is the biggest part of the problem, but it also holds the key to solving that problem.  If there is no "structure" above a bishop that would allow personal accountability, then I think the situation puts the cure squarely in the hands of the bishops themselves.  They have a "blank slate" that should allow them to adopt whatever system of accountability they may choose, be that in the form of a tribunal, some kind of Canon-law-based court system, etc.  

If their argument is that only the pope can do that, then their own logic pretty much damns JPII, Benedict, and so far, Francis, none of whom seemed willing to hold these guys accountable.  The effect leaves  double standard in place.

The current makeup of the commission (without survivors) pretty much guts the team of what credibility they may have once held, although I think by the lack of any meaningful change coming from the commission, they had long ago given it away.