How much of the Pokémon Company does Nintendo own?

This appears to be a muddled area of inquisition. This is mainly due to Nintendo having an ubiquitous amount of stake in one of the other companies that own the Pokemon corporation. read more

In short, Nintendo owns roughly 33% of Pokemon, while two other companies own the remaining 66% (assumingly equally). However, one of those companies, Creatures, Inc., is the aforementioned business that Nintendo has an alleged undisclosed percentage of stock in. For pure speculation if the big N owns over 50% of the Creatures company, then they would virtually own 66% of Pokemon. read more

For Wii U on the Wii U, a GameFAQs message board topic titled "Does Nintendo own the Pokemon Franchise or Game Freak". read more

No. The third partner is Creatures Inc., not the Pokemon Company. The Pokemon Company was established by the three parent companies to manage the IP with each of the parents owning roughly 1/3. Pokemon products are labelled something along the lines of "©2016 Pokémon. ©1995–2016 Nintendo / Creatures Inc. / GAME FREAK inc.," indicating jointly held copyrights. read more