As a Fedor fan, through and through, I would make this observation: I don't think it's a fair comparison to stack Fedor "then" up against UFC champs "now."
The reason being that MMA has continued to evolve day after day, year after year, since it started. Today's mixed martial artist is a far more evolved and well rounded fighter than they were in Fedor's heyday. Everybody these days is studying aspects of Wrestling, Muay Thai, Brazilian Jiu Jutsu, and so on and so on.
In Fedor's day, most mixed martial artists were basically from either one style, or maybe 2 like wrestling/boxing. Fedor himself was trained in Sambo, although he may have cross-trained in the later parts of his career (I'm not enough of a Fedor geek to know for sure.)
What made Fedor great was his adaptability. He could adapt his style and overcome whatever style his opponent brought. Which supports a theory of mine that there is no superior style of Martial art, it's all about the individual practitioner.
I, too, wanted to see Fedor sign with and fight in the UFC - and was disappointed when he didn't. BUT, to question his legitimacy because he never fought in the UFC is just bullshit. In most weight divisions, the PRIDE roster was stronger than what the UFC had at the time. Especially in the LHW and HW divisions.
SO - was Fedor the Greatest of All Time? The only answer I have to that is "Unquestionably and Absolutely." (Anderson Silva never came near the level and length of dominance Fedor had.) But - Would he stack up well against today's HWs? Well, honestly, probably not. But (to borrow from another sport I love dearly) If you brought a Top Fuel Dragster from the 90's, and matched it against a Top Fueler from today - It would lose every time, because the cars have gotten faster over the years. It's not a fair comparison.