Small recap of how Nintendo makes money off of Pokemon.
Pokemon Copyright
The copyright is owned by Nintendo/Creatures/GameFreak. This covers the overall universe and design of Pokemon - as the original game was created by GameFreak but Creatures and Nintendo were involved in assisting and producing the game. Revenue from copyright goes to all 3.
-Nintendo/Creatures/GameFreak
Pokemon Trademark
This is where Nintendo made out as they are the sole owner of the Pokemon trademark. This means anytime the name appears on a product, Nintendo is entitled to revenue from it. This was probably the condition for publishing and advertising the original title.
-Nintendo
Pokemon Publishing
Nintendo used to publish all the Pokemon games, later on they established TPC as the main publisher while Nintendo was the co-publisher or distributor providing the channels. For Pokemon Go, Niantic is technically the publisher handling the monetization.
-The Pokemon Company / Nintendo / Niantic (for Pokemon Go)
Pokemon Production
The Pokemon Company and Nintendo always have production channels on every piece of Pokemon software. GameFreak and Creatures do not involve themselves in production on outside games. Hitoshi Yamagami from Nintendo (also Fire Emblem producer), handles the game production end from Nintendo on all Pokemon titles.
- The Pokemon Company / Nintendo
Pokemon Development
This is where a myriad of developers are involved. GameFreak for the mainline series, and Creatures with spin offs. Other developers like Chunsoft, Ambrella, Genius Sonority, and Niantic have been involved with different entries. Nintendo has also internally developed several Pokemon games and peripherals like Pokemon Stadium, Pokemon Box, Pokemotion, and Pokemon Go Plus.
- Nintendo / Creatures / Game Freak / Genius Sonority / Ambrella / Chunsoft / Niantic
Pokemon Companies
Lastly, Nintendo owns stakes in several of the companies involved in Pokemon. Nintendo owns stakes in The Pokemon Company, Creatures, Genius Sonority, and Niantic.
- Nintendo