I also believe they probably do, because if you want a game along those lines then Nintendo consoles still make the most sense. However, the existence of Donkey Kong I feel hinders your point rather than helps it. Donkey Kong co-exists alongside Mario mostly because of how popular the characters have been over a long period of time. They have widespread recognition and represent Nintendo as a whole on only a slightly lower level than Mario, Zelda or Metroid. Nintendo has tons of IP they are reluctant to use these days (such as F-Zero), and many of these are in areas that their console actually has noticeable gaps to fill. I don't see why they'd be more likely to select an IP that would come behind Mario, Donkey Kong and even Kirby to create another game in line with those that they already have plenty of.
With MS it's the opposite scenario. I can see them possibly reviving Banjo, Viva Pinata or Kameo, in order to flesh out their first party offerings a bit. I find it less likely that we'll be seeing much from Perfect Dark, as a result of them having Halo and Gears. If Nintendo had all of Rare's IP currently, I would expect that we'd already be seeing a Retro developed Perfect Dark.