It does seem pretty drastic...especially when the rider who wins the GP could receive less points than the guy in second place.
However...
Last year, a guy could qualify for the semis with 9 points, get a second in the semi, get through to the final and win it - therefore gaining 25 GP points.
Where another guy could have qualified for the semis with 15 points, then wins his semi but then comes second in the final - getting 20 points.
With last years system the rider who was the best overall didn't necessarily get the most points. Whereas with the new system, he will do.