The biggest problem for Fedor's legacy isn't his performances, but his management. By keeping him out of the UFC and then, even after signing with Strikeforce, dodging Alistair Overeem, M-1 Global gave legs to the argument that Fedor was ducking top competition. They tried to make Fedor a promotion unto himself, and in the process they kept him out of the fights fans really wanted to see.
That's the worst part. As Fedor fades away, it's hard not to wonder what he might (or might not) have been capable of back when he was at his most capable. Just because he loses a few fights in his mid-thirties, that doesn't mean he wasn't one of the sport's great ones. Few fighting careers end on high notes, after all. That part is nothing new.
What will hurt Fedor more than anything is that, when the time came to choose between forging a legacy and cutting a deal that would let him splash the words 'M-1 Global' all over the cage, he chose the deal. Or at least, he chose the people who chose the deal on his behalf. He wanted it his way, and that meant more to him than how he'd be remembered. Now that he's gone, at least from MMA's biggest stages, don't be surprised if that's a part of what people remember.