With the Game Freak-developed Tembo being not only on non-Nintendo platforms, but will not be on any Nintendo platforms at all, Nintendo owning more than 50% of Game Freak's shares means nothing. And it does not help when Pokemon creator Satoshi Tajiri was the executive producer of Tembo. No wonder the late Takeshi Shudo and subsequent directors of the Pokemon anime after him made sure that Ash Ketchum never wins the Pokemon League, especially when Ash was called Satoshi. It's like the directors of the Pokemon anime disliked Pokemon creator Satoshi Tajiri, or any character based on him, and for good reasons.
Maybe most of us have never played Pulseman, another Game Freak-developed game which was published by Sega just like Tembo. However, most of Game Freak's non-Pokemon games never left Japan, meaning that we were unaware that Game Freak made games that were on non-Nintendo platforms during the Console Wars of the 1990s, which could jeopardize any relations between Nintendo and Game Freak should this truth ever be made known to the general public. This could also explain the absence of Pulseman in the Sega Superstars series, especially when Game Freak developed Pulseman for the Sega Genesis/Mega Drive.
Game Freak was also said to be the reason Pokemon had been a licensing nightmare for the Super Smash Bros production crew, and Masahiro Sakurai claimed that acquiring the license to include Pokemon characters in the Super Smash Bros games was harder than that of third-party characters, including the theoretically impossible ones.
Finally, Game Freak was the reason there was no Pokemon-themed attraction in Nintendo Land, which can also explain the lack of actual Pokemon cameos in many of Nintendo's games. It seems like acquiring a license from Game Freak is actually far harder than acquiring a license from a third-party game studio, especially for character cameos and crossovers. So much for Pokemon being published by Nintendo...