Sega's two biggest development teams are the Sonic Team (who, obviously, make more than just Sonic) and AM2 (Yu Suzuki's crew; fighting, Shenmue, and everything in between). Amusement Visison and the Sonic Team are the only teams who express love for the Gamecube. Yuji Naka was apparently very annoyed that Sonic Heroes would have to be multi-platform, a decision that no doubt came from the higher ups. Amusement Vision is tied in to the Triforce and are the main (pardon the pun) "force" behind the new F-Zero. Of course, they're also responsible for Monkey Ball. Yu Suzuki, however, has always expressed his disinterest in the Gamecube. When asked once whether or not Virtua Fighter would ever appear on Gamecube, he remarked "I don't think it would work well for the Gamecube's image. Maybe Virtua Fighter Kids." Sega eventually committed him to Virtua Fighter Quest, a game that has mysteriously vanished off the radar in the last year.
Second parties tend to not get treated well by Nintendo. If Nintendo were to buy Sega, they'd pretty much lose all independence as a company and become assimilated in to Nintendo. Granted, this would be the same thing if they were bought by Sony or Microsoft, so they stay as a third party. Nintendo likes to check in on second parties and often tinker with their games if they think it's not going well. Those of us who are old enough to remember can recall a time when Nintendo did this to third parties and ended up pissing a lot of companies off. All of Nintendo's current second parties never started off as big companies, so they are happy working with Nintendo to make games and such. After all, if you made Metroid Prime or Eternal Darkness, you'd be pretty damn happy with yourself. Imagine for a second that your the creator of, say, Jet Set Radio. You had this great idea, and all of a sudden, Miyamoto busts in (with a banjo simply because I always picture him with a banjo in his hand) and tells you what tweaks to make to the game. If you're a young and aspiring game developer, this would be the greatest experience of your life. If you're a seasoned veteran, not even Miyamoto should be allowed to tell you what to do (from your point of view, of course; though, I do have an inkling that the Holy Father of Gaming is going insane now). Plus, Sega is making more money as a third party than they were as a hardware manufacturer. Nintendo doesn't want to buy them, Sega doesn't want to be bought. It works out well.
Now if only we could just convince them to give us some exclusives...
-- ShockingAlberto