Yeah there's just not any truly sound way to rank people in a game that has so many hidden bosses. The big problem is many of these players not only don't get ranked, but they also get atrocious seeding, making it extremely difficult for them to prove their worth on a national level the few times they travel. That leads to misleading results, which makes the seeding just as bad, and the cycle continues.
The next big problem with the rankings is that the WCIOM panel is almost entirely WC. Ok, we get it. It started out there, they have the best regions, etc. But there should be an effort made to include at least one person from every region on the panel. Yes, every region. Cutting down bias is the first step to creating a solid rankings.