Didn't some of the American members of the Sonic 2 team also say Naka came across as a douche and whenever content got cut, it was normally something from the American half of the development team?
There's also that infamous story of Peter Moore telling Naka to fuck off when he gave him shit over some negative focus group testing.
Yep, most of the content cut from Sonic 2 was from the North American staffers that were working on it. To be fair to them, though, based on the prototype versions of Sonic 2 that are out there, their content was also cut for being both of lesser quality and for possibly being behind schedule (unfinished levels like Hidden Palace and Wood Zone apparently went untouched for months without any significant updates).
You do remind me of two other examples, though:
Yuji Naka and Hirokazu Yasuhara apparently butted heads a lot. Naoto Ohshima handled character designs, Yuji Naka handled game logic and coding, leaving Yasuhara to be the man who focused on levels. He did a lot of art direction and even built many levels himself. He also was a general Director, overseeing many of the other aspects of how the Genesis Sonics were put together.
Between them, Naka, Ohshima and Yasuhara were the combined heart of Genesis Sonic.
After S&K was finished Yasuhara left Sonic Team because he and Yuji Naka didn't get along. Yasuhara stuck around Sega for a while after that, bouncing around between various projects (and even helping out on a few Sonic projects; I think he was attached to Sonic R, for example, and there's concept stuff he did for Sonic X-treme floating around out there).
When Yasuhara left Sega some time in 2001 to join Naughty Dog, Yuji Naka disliked him so much that he actually made a public statement that he felt Yasuhara had become "useless" to Sega. (Yasuhara now works at Nintendo.)
Rumors float around regarding Naoto Ohshima's relationship with Yuji Naka, and that a similar thing possibly happened. According to the rumor, after the original Sonic Adventure, Naoto Ohshima and Yuji Naka got in to an argument over where they wanted the franchise to go for Sonic Adventure 2. Ohshima reportedly quit because Naka wouldn't listen to him.
Some credence is lent to this rumor - a couple years later, when Sonic Team released Sonic Adventure DX for the Gamecube, Naoto Ohshima's name was completely scrubbed from the game's ending credits sequence. In the original Dreamcast release, he's credited for a few things - notably being the director of the game's pre-rendered CGI sequences - but his name is completely gone from the DX release.
It would seem as though Yuji Naka might've driven away everyone who made those 16-bit Sonic games what they were.
At least he got a Ferrari out of it, though.