I don't know if it hurts Fedor's legacy. I think it puts it in perspective. It kind of depends on what you mean by all time great. Does that mean domininant in their time or a head to head in their prime matchup. A similarity could be drawn with boxing. Take Jack Dempsey, one of the first major champions in boxing. He is still considered an all time great, but his size and speed could compete with that of the top HWs like Lennox Lewis or Evander Holyfield. However on an all time greats list he would definitely be ahead of them.
Fedor's legacy is that he was the best HW of the PRIDE era. Yes he was protected after the fall of PRIDE and that may hurt him somewhat. I don't think he will go down as the greatest fighter of all time or even the greatest HW, because mma is still so young. The sport simply passed Fedor by. Ali lost 3 out of his last 4. Two were to less than stellar opponents in Berbick and Spinks. Most fighters fight too long. A very few walk away when they should.
Hit the nail on the head. Nobody remembers Joe Lewis' or Alis losses unless it was a war. The losses at the tail end of their careers never really get noted as the fighters are on the decline.
As for Fedor, I really don't care what peoples personal opinions of him are, he is without doubt, one of the greatest ever. Top 3. Easy. Just because the level of opponent has grown stronger while Fedor has got older doesn't mean anyone should think anything less of him. Its called progression. How can anyone really expect Fedor to be undefeated all his career when MMA is progressing and developing so fast?
I think a couple of people mentioned fickleness. Its f*cking epidemic in the world of a MMA fan. People will be hanging of a certain fighters balls one month, next month the same fans will be denouncing the fighter, claiming him to be a 'can' or whatever. I don't think its gonna change. I think its down to each individual fan. Nobody wants to be wrong. Everyone wants to appear knowledgeable. Thats why minds change so often. People are too worried about other peoples opinions.