I don't quite understand where you are getting at, but I'll try explain it to the best of my ability: Friends is one thing, business is a whole other issue.
Naka-san's frustrations with SEGA were presumably due to the fact that in a company, the more high up you are, the less you are involved with actual development. But no matter how high up you are, you still have something that you answer to.
And Yuji Naka's transition from Sonic Team head honcho to Prope allowed him to have his creative freedom and not be restrained. This is not unsual, it's a fairly common occurence in the world of business. I'm sure there are personal frustrations too, but at the end of the day, it's just business.
@Barry
Oh, OK... After a while I stopped hearing about the game, I actually though it was out, but only in Japan. In tht case, I feel for Naka-san. The game looked great, but the Wii is no longer a relevant platform...