I know, that's why it seems like it would be a bad investment to sink a lot of money into a game where you did not own the IP. It would be more than a bit atypical. Look at how Sony will fund a game proposal from a small developer but they always ask for the IP in return. Otherwise, there are a lot of murky areas, legally speaking.
It makes me think of the WWE's recent practice of forcing performers to change their names when they're signed, with the WWE owning the new brand. There have been so many back-and-forth law suits with regards to who has the rights to what that it seems like it will never end, with CM Punk and the Honky Tonk Man joining the parade.
Perhaps Nintendo have bought it, but never bother to announce and make it clear, and that detail is hidden somewhere that no one's bothered to look. There's also the possibility that SEGA wanted to hold onto the IP for dear life (for whatever stupid reason, even thought they obviously buried it), and they may have kept it at a steap discount to Nintendo on getting total-rights over the game. If there was some pre-developed game, for example, and Nintendo stepped in and said:
"We will fund this but it will be exclusive. Period."
And SEGA said:
"Okay, but we get to keep the IP but you don't have to pay for whats already built but you have ownership over it."
Then both companies could walk away decently happy, Nintendo pays less (potentially a lot less, depending on how far along the game was before SGEA pulled the plug), SEGA keeps their IP... for whatever reason.
I don't really see a reason for SEGA to keep this IP, when they're obviously just itterating and burying new IPs until they find some sort of "big" hit, while recycling Sonic and Aliens. It'd be interesting to see if Nintendo may not have ended up shelling out much less than expected on the title while also securing exclusivity over it entirely just because SEGA wanted to keep the IP. It really doesn't make much sense, otherwise, why Nintendo would just take the whole thing in its entirety if they also went through the bother of porting up Bayo1 and getting rights to it too. (We at least know from Kamiya that Nintendo has full control and rights over Bayo2, so that's not even a gray area, they are the sole owners of the title and gamecode.)
So either they do own the IP, now, or they got a deal from SEGA over not buying everything outright and cutting out SEGA entirely.