Ok so I waited a little while to process the main event to give my unbiased opinion but here's how I feel. I thought Naito should have won the IWGP Heavyweight Title but for a different reason than what everyone is saying in this thread. Most people in here simply just tired of Okada with the belt and want someone new with it, it is what it is. I understand why Gedo pushes Okada as much as he does for business reasons and marketing reasons... Gedo is booking how Vince booked Cena and how they book Roman... it's "best for business".
My main problem with Okada retaining is that it destroys everything they built Naito up to be currently: a man who's not the office pick who has his own identity that has a cult following and is open about how he doesn't like certain things that the company does... Naito is the modern day rebel that's following the foot steps of Steve Austin, CM Punk, Daniel Bryan and to a certain extent Jake "The Snake" Roberts with his cool calm yet dangerous demeanor. With those guys (Jake is questionable) they all had a defining moment where they defeated what many people considered the best and etched their moment and legacy in stone (Austin beating Michaels at WM, Punk beating Cena at MITB, Daniel Bryan standing tall at the end of WM30) and this should have been Naito's definite moment because any other time won't have the same luster as today did and it won't have the same impact.
Another thing that was wrong with the decision to let Okada retain is that Wrestle Kingdom 12 main event was supposed to be the match that made Naito's cypher complete and make the full circle story of "The Death of the Stardust Genius.... the Rise of the Ungovernable One" have a satisfying ending and to start a new chapter in his career. Four years of Naito crawling from his grave reinventing himself abandoning what he once believed in destroying the heroes that he once looked up to just to once again earning the chance to achieve what he couldn't do 4 years ago to avenge his own death.... and storyline wise he couldn't do it and it leaves a sour taste in everyone's mouth that believed in Naito. Realistically a loss for Okada tonight wouldn't have hurt him, he's had a legendary run and a loss to Naito would have been a honorable loss as well as been looked at as "The self governed influential outsider defeating the hand picked golden boy company man". I'll end this random rant by saying now we know how we would all feel had Apollo Creed defeated Rocky Balboa in the rematch in Rocky 2....