As a huge fan of both fighters, I go back and forth on this.
They both have the most savage GnP in the history of the division, but Fedor's armbars would be a significant threat to Cain in the guard.
Cain has the height/reach advantage, but Fedor's career was made by dominating bigger opponents. Non-factor.
Cain has very good punches with no wasted movement. They're more precise than he gets credit for. But they're not neccessary meant to KO opponents, just hurt them or distract to get a takedown.
Fedor's shovel punches are wide, loopy, and very powerful and can easily KO anyone who has ever fought. But, he's open to straight punches, and even in his prime Fedor was hit with straight punches regularly. He just weathered the storm.
Fedor's legkicks are savage - just ask CroCop. While Cain's legkicks... well, I can't think of one that was ultimately effective in leading to the end of the fight. Might as well give that one to Fedor.
The absolute biggest factor that separates them is endurance. Cain has earned the 'Cardio Cain' nickname because he could easily fight for 5 rounds. Fedor, on the other hand, has never fought five 5-minute rounds, BUT that first 10 minute round in Pride was murder. Fedor's basically a middleweight with ALOT of extra muscle and fat, and in a five-round fight endurance would be a HUGE factor against someone with better endurance. But, this is only a factor is the fight would go into the 4th and 5th rounds. Most of his victories are by KO or Submission before the 3rd round. He only has a few fights that went to a decision.
I could go on and on further into each factor I mentioned, but is anyone goong to ready a 5,000 word post?
I picked Cain in the poll upon entering the thread, but after typing this up, I wish I could change my vote to Fedor.