I've thought about the Nintendo and Sega thing, but Nintendo already has so many quality platformer franchises that Sonic wouldn't be much of a benefit to them in that area (though they'd be a benefit to Sonic). Perhaps Sega's expertise in racing games would be advantageous, but one (if not the) of their best outtings was taking on Nintendo's F-Zero series. Most of their ips are weak, and the ones that aren't tend to be in genres where Nintendo does it better.
SE, however, has a diverse set of ips (relative to Nintendo). Also, their work together in the past has been fantastic, and with the magic Nintendo touch SE should be able to get its act together. They have clearly mismanaged a significant number of their IPs.