I feel your pain dude! I started getting into Pride right around the time Cro Cop won the 2006 Grand Prix!
Yeah it's to bad but back at that time I wasn't HUGE into MMA like I am now and I was quiet happy with TUF and Matt Hughes, Tim Sylvia and Chuck Liddell etc. I mean how the hell would I even know? I had never seen anything on TV about Pride and that was back when I first got the internet.
It's way more complicated than that.
The Yakuza had been involved in Pride essentially since its inception, and everyone knew it (including the Fertittas, when they bought the company).
The entire history of the organization is incredibly shady. The "suicide" of Naoto Morishita and the rise of Sakakibara, who was a little too friendly with a lot of Yakuza leaders, and seems (to a lot of people, myself included) to have basically become a puppet for the Yakuza.
Really, though, the only thing that we don't know was the exact extent of Yakuza involvement in Pride, but it was always clear (whether from watching managers like Ken Imai take over the contracts of major fighters, or watching guys like Sakakibara set up control of the organization) that the Yakuza had some hand in dealing with the behind-the-scenes stuff in Pride.
As far as why it wasn't carried on by the Fertittas, there are a few reasons that are (simply) better than the observation that there was mob involvement (I mean, the Fertitta family has a history, too, though that tends to be blown out of proportion a little bit). Firstly, taking in the entirety of the Pride roster would have been impossible for the UFC, as Pride was losing tons of money (indicated by the fact that the UFC bought the organization for a reported $70 million, which is basically pocket change). Operating costs were not worth potential benefits.
Secondly, there were a number of lawsuits filed about how the UFC would operate Pride should it keep the organization running. Sakakibara filed one of these lawsuits, though (from what I understand) there are many, filed by a handful of parties.
That said, it was an organization that put on many of the best shows MMA has seen so far, and it has a lot to teach western fans.
The institution of the yellow card is one thing that could be huge in western MMA that we don't seem to talk about very much. And then there are the fights themselves, and I could ramble on for days about them, but I'll just say that there's nothing better than a great war with a story behind it, and Pride made those happen.
This is just wrong.
The Japanese know how many of their business are built into syndicates that deal with organized crime. The way that Japanese syndicates operate is totally different from the way American gangs do, much more like the business-based gangs of the 1920s.
They deal with illegal enterprises, but many of the syndicates are respected by the Japanese.
Moreover, it's hard to say that the Japanese "general population" didn't know about the Yakuza influence before. The Yakuza have a long history in professional wrestling in Japan, and the connection between Japanese professional wrestling and MMA is pretty fuzzy from a fans standpoint.
The notion that Pride had a negative public image in Japan is kind of ridiculous. They weren't that popular because they weren't putting on huge shows, but they had always known about the operational stuff in the same way they know about the Yakuza's involvement in local liquor stores.
Towards the end of Pride, they were not drawing the same kinds of crowds they should have been, and were paying their fighters larger amounts of money than they could reasonably afford, so they were headed towards bankruptcy. It wasn't that they had an illegal business, it's that they didn't maintain the quality of the product and kept the fighters salaries pretty damn high.
It's just to bad I wonder what the MMA world would be like if Pride was still around. I thought I remembered someone telling me that the owners death was somehow involved with Yakuza and it was actually murder, but hey how the hell would any of us ever know.