Is Ali fighting the best RIGHT NOW? Nope, he's retired. Let's say Fedor retired right now. Would he still be getting the same hate? Yup, you bet he would. You know why? People find reasons to hate on great fighters and question their legacy/career, it happens to all great sportsmen.
If Fedor retired last year, would we be having this conversation? Yup, cause people would be still saying "Fedor only beat Sylvia and Arlovski before he retired", even though they were both highly ranked. Why? Cause people will find a way or reason to disagree with someone's career.
What Fedor has done in his career cannot be forgotten, and if he was retired he'd be getting the same crap now as he would if he was retired. Just becasue he's still fighting does not mean that his legacy or career or anything is even slightly tarnished. What he's done is done, and what he's done is amazing and will always be amazing, no matter what he does right now or in the future, retired or not retired, here or there, it does not matter.
A legacy is what have you done in your career, and Fedor's career is being praised right now to this day by Legends, P4P contenders, current and former champions, as well as a very, very large portion of hardcore MMA fans as the best in the sport's history.
His legacy is set in stone, what he has done is there. What he does from now on will always be questioned, as it would be with any other great fighter, but that does not remove the past or his legacy as a whole.