The marketing and development divisions being funded lend different levels of priority to Nintendo. The case of Bayonetta 2 is the most obvious example. Bayonetta 2 would not have existed ever without [a company like] Nintendo's involvement. But in the case of something like Ninja Gaiden 3: Razor's Edge, Nintendo's involvement helped that game happen but a contribution to the marketing budget and bearing the publishing burden allows Team Ninja to develop and Tecmo Koei to fund that development unhindered, and in exchange, Nintendo's obviously not gunna market or publish the game for other consoles, so a timed-exclusive deal is made. When that deal is over, the marketing assets are already available for use; all that's left is to put an Xbox or Playstation logo on it. Having said that, Ninja Gaiden 3: Razor's Edge being published on Wii U by Nintendo doesn't disqualify it from being published anywhere else.
Ubisoft is a big company, and I'd imagine they don't have any problem funding this project themselves, but they've been playing things pretty safe lately. Ubi's idea of safe is also homogenizing their games to the point where development of games like Assassin's Creed and Watch_Dogs use the same engine and similar assets by the same development teams across different titles to speed up development. Notice also how The Division and Ghost Recon: Wildlands look incredibly similar?
Ubisoft also said a while back that they'd be making everything open world because that was the trend that sold and every game needed that "open world innovation" (Which is also my fear for Zelda because the open world bubble has popped already and nobody's picked up on that yet, and I don't want Breath of the Wild to be affected by that and viewed as 'too little too late.') Bottom line is they're more likely to green-light and fund games like Assassin's Creed and Watch_Dogs because of that whole content per hour mandate, over games like Rayman Origins and Child of Light which have definitive beginnings and ends. You'll see less risks like that being taken by Ubisoft over time.
Having said this, Watch_Dogs 2 severely underperformed, so let's see how Ubisoft's outlook changes, if it will at all.