Sega was really the best choice, all things considered. This might even be a good thing for Sega. I could see Atlus helping them with the Yakuza games overseas, for example. Or maybe even translating/porting older games, like Sega's Saturn library. Things like that. And they'll still keep making their own games.
Whoever said Sega ran their own consoles into the ground was way off the mark. The only systems they really did that with were the 32X and the Saturn. The Saturn was only botched because Sega released it here during E3, on the same day they presented it, without letting retailers know, so they broke a lot of trust with that.
The Dreamcast became unpopular after only 9 months through no fault of Sega's own. It really had to do with the PS2 coming up. Everybody was so hyped about it. Even if Sega had waited to release the DC, or had released it here the year before like in Japan, the same thing would have happened. It was just terrible luck.