Interesting effort. I'd like to see their rankings within each division. I generally find FightMatrix rankings better than the UFC's, because they're mathematical.
However, P4P will always be subjective, because there's no possible way for any of these guys to ever face each other (for the most part) and one could argue that HW MMA and BW MMA aren't even the same "game". The skills a HW can physically execute and the dangers a HW faces are not the same ones a BW does. It's like having different chess leagues with different kinds of opponents for whom it's physically impossible to face each other, and then trying to compare them. It's the same reason WMMA rankings are separate from regular MMA, they're separate sports in a way. On top of that, you have different promotions with different levels of competition (*cough* MousasiAokiPitbull *cough*)
Add to that, that MMA is not like tennis or chess, where "flukes" are basically impossible. Poor decisions, flash KOs, impressive/unimpressive performances, championship/non-championship fights, steroid accusations, etc, complicate the perception of MMA performance a lot. There isn't even a single unified criteria for P4P that everyone agrees with.
With all that said, GSP is the GOAT.