I'm okay with saying that Fedor is the greatest HW during the Pride era, but not the greatest fighter now or ever. He's lost that top position not because he's over the hill, but because he's not fighting the best. If, for example, he fought in the UFC and won the belt, then I'd feel comfortable calling him the greatest now and the greatest ever.
We seem to be going in circles. What's done is done. Fedor beat fighter X at such and such date. The question is whether that fighter is or was the best at that time. Arlovski and Sylvia wouldn't last long in the UFC. Neither Cro Cop nor Noguiera are serious contenders. Werdum is certainly not the best, wouldn't you agree? I think Werdum as as good as the above fighters, but I wouldn't say he's the best.
Ali fought the best at Fedor's age, and won. Fedor is not fighting the best at Ali's age, and lost. *Ali was still beating the best in his mid 30's, that's why his legacy is what it is. *Fedor's legacy is not over yet, and it's headed towards the wrong direction.