And that's because it was never designed to qualify all the world's best. If it had been, you wouldn't have had the continental qualifiers. It was designed to get a variety of nations represented, regardless of how good the riders were. People today still don't get how flawed the old system was...
We've had a number of different formats. Prior to this one, actual race points counted, which meant that a GP winner often scored fewer points than the riders behind them. Now, the system guarantees that the winner scores the most points - and that annoys most fans.