Take a fighter. Match him up hypothetically with every single fighter in the top ten of their weight class. Take the average of the gamblings odds for each match up.
The best fighter in a weight class is the one with the best over-all odds. The best fighter P4P in the world is the fighter with the most tilted odds, at least for ranking purposes.
The reason that Fedor is the number one fighter in the world is he'll get MASSIVE odds in his favor against any heavyweight in the world. Gonzaga? Couture? Arlovski? Barnett? Nog? Cro-cop? He'd probably get above 4:1 on every HW in the world.
Hughes? The odds would be AGAINST him or next to even versus the top 5 welterweights in the world. Gomi wouldm't have nearly the gap fedor has. Anderson Silva and Hendo are in the same situation.
NO ONE can even close to producing lopsided odds like Fedor, no matter what you adjust for ("styles make fights","TUF audiences' ignorance","the hype from the nuthuggers", whatever.)
It's far from a perfect system, but it's a better system than people just throwing around their bullshit speculation about who they think would beat who.
I would use the following factors to determine who is currently the best mixed martial artist in a given division: (1) number of wins, (2) number of losses, (3) how dominating the fighter was in victory and how dominated he was in defeat, (4) whether the fighter has avenged his losses, (5) quality of competition, and (6) time elapsed since performance.
Considering these factors, I think it is difficult to argue that Fedor is not the top heavyweight.
Active of not, unless someone exceeds his accomplishments and record, he will remain #1. If you are a fighter, your ranking has nothing to do with someones inactivity unless you can match his accomplisments.