I'm going to side with some of the people in this thread and absolutely believe Playtonic should remain independent as a third party company and publish for what they want to. First off, I'm in the camp where I don't have a Wii U, though I do have a 3DS. One of the reasons I've held off getting a Wii U (though I do admittedly have a 3DS) is partially due to Nintendo's stance on region locking, which has been an issue with me. Both Microsoft and Sony have moved entirely away from this practice, while Nintendo still stands by this. This also could potentially lock out users who want to play Yooka-Laylee that are in an unsupported localization region if Nintendo decides not to publish in that region.
Also, for me, it's also an issue where outside a couple games, I haven't had felt a reason to get a Wii U, though the library is slowly increasing, making me thinking more about getting a console down the road. I do, however, own a Playstation 4, though a mid-tier PC as well, but I absolutely plan to go for the Playstation 4 version of this. If say Nintendo were to snap up the rights to this, I'd be one of many players who would be locked out from playing this game, until when I could maybe put down money for a Wii U. Even then, I'm leaning towards getting a foreign Wii U which could potentially lock me out of the game still if there's no localization decision for that region.
Either way, the more systems the game is available on, I feel the better chance players will be able to play this game and be able to find enjoyment on. Limiting the audience to one console is never a good thing, as it always locks people out of a chance to play it. Consoles aren't cheap, as well there could be other reasons why people don't have multiple consoles (such as space issues, which I'm currently running into at the moment).