Here's the way i see it:
There's an obvious gap of skills between a 2003-2005 Fedor and a current day Cain Velasquez.
Fedor at his peak actually passed his tests better than Cain. They both fought a large striker when they were working their way up to the top. Fedor fought Schilt, Cain fought Kongo. Both outgrappled and defeated their opponents, but the difference is that Cain was dropped twice while Fedor dominated that fight completely.
When they both faced an elite striker with TD defense (Crocop/JDS), Fedor won decisively, while Cain was KO'd and needed two more fights more in order to prove he was better, and when he did, it was in a terrible sloppy brawl in which both fighters gassed in less than 2-3 rounds.
These are nothing but little signs, not as for who would win the fight, but about their skills as fighters. Fedor was more skilled than Cain, and far more well rounded. That's just evident. He was also visibly faster and more powerful, a better striker and better overall grappler.
Now Cain defeated Bigfoot, who defeated a nearly retired Fedor, but that really doesn't say much other than Fedor being far past his peak, while Cain was/is probably in his. Basicly the same as Ali losing to Berbrick and Tyson defeating him. It doesn't really say much about how would Ali and Tyson match. MMAth has proven to be useless countless times.
Now when it comes to a fight, could Cain had outwrestled Fedor at his peak to win a decision?
Perhaps, but not likely. Thowing 500 "pillow fists" (and by this i mean he's a volume puncher, more than a power puncher) per round would leave Fedor with too many openings to catch him with a sub. Fedor had too many tools at his disposal off his back: subs, sweeps, great hips, excellent defense from the bottom, etc. Cain's GnP is all about volume of punches, he's not that powerful, nor he cares about picking his shots. Problem is, Fedor, was extremely hard to gnp. In fact before 2009, he never received any significant damage while on his back. He was also very durable. Cain wouldn't finish a prime Fedor, yet Fedor could finish him, anywhere.
The stand-up isn't even close. Fedor was clearly better; faster, more powerful, more explosive, more accurate, more unpredictable, etc. He lands a bomb on that chin and Cain goes down. Cain has been rocked/dropped several times already, and Fedor was a hard puncher and very explossive. I don't think Cain would pose much of a threat in this department, not even if he mixed it up. Fedor wasn't afraid to be on his back, and he would also mix his striking with upper body takedowns, and he did this very quickly.
Cain is a fighter that comes foward and likes to dictate where the fight goes, but so was Fedor, and a fighter like him wouldn't let Cain fight his fight, he would come at him and pressure him as well. Cain has shown most of the times he has good cardio, but last two times vs. JDS he was breathing heavy inside 2-3 rounds and while he was throwing a lot of punches, they weren't that powerful. Problem is, neither JDS, Kongo, Brock, Rothwell etc. had the skills to capitalize on Cain's mistakes while on the ground, but Fedor did.
Bottom line, I'd think Fedor's chances to win would've been clearly superior, as he had a lot more tools at his disposal to win and/or finish the fight, and was clearly a better overall fighter.