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 a rematch 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 rounds.
Theses are nothing but little signs, but they say something when it comes to skills. Fedor was more skilled than Cain, and far more well rounded. That's just evident. He was also faster and more powerful, and had a bottom game second to none.
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.
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 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, excellent defense from the bottom, etc. He was extremely hard to gnp. In fact before 2009, he never received any significant damage while on his back.
The stand-up isn't even close. Fedor 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.
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 time vs. JDS he was breathing heavy inside 2 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, we will never know what wouldv'e happened, but I'd think Fedor's chances to win would've been clearly better, as he had a lot more tools at his disposal to win and/or finish the fight, and was clearly a better overall fighter.