Pride started out as an outgrowth of Takada's pro wrestling career(which was going badly, UWFI had folded, New Japan jobbed him out and the Gracies beat several ex UWFI fighters) basically built on the idea that a match with Rickson would be real because Gracies wouldnt do works. The very early stages some of the other fights looked questionable but honestly I think the fact they looked questionable tells you that pro wrestling could never pass as MMA, look at Takada vs Kyle Sturgeon and it looks a lot like a UWFi shoot style pro wrestling match just pushed a bit more towards realism and much shorter, look at the worked RINGS matches like say the Volk Han/Tamura fights and its clear this isnt real fighting.
Past the very early Pride shows I don't think theres any question of there being pro wrestling matches on the cards, there is some question of fixed matches, Coleman/Takada tends to be viewed as such but honestly people could see that pretty easily as well and the fix was not kept under wraps at all, Gary Goodridge claimed Ogawa's corner tried to pay him to drop the fight(althougbn Gary clearly didnt, you can see he's trying to KO Ogawa) as well so really you can't stop people speaking out.
Really to me the issues with bias in Pride are not much different from the UFC, potential bias in terms of match making and reffing/judging. In Fedor's case though I would argue he was never really Pride's chosen son until very near the end of his career, Nog was more popular back when he won the title and Mirko was more popular afterwards, you look at the judging and reffing in Fedor's fights and nothing looks dodgy to me in Pride, every decision is a clear win for him and no questionable reffing calls, indeed the most questionable calls arguebly went against him when the ref stood up the Mirko fight quite often in rounds 2/3.
Plus of course the idea Fedor started loosing as soon as Pride ended or as soon as he came to the US is nonsense, he didnt loose until 3-4 years after those things, he beat 2 of the 3 biggest name UFC HW's and when he lost it was to another ex Pride HW.