They profit by what they own is my guess, so if the own 53%, thats the revenue they get from Pokemon games.

Pokemon is owned by Game Freak, Nintendo, and Creatures Inc. I'm not sure how profits are divided up between the three companies, but I assume GF has a lot of control over the franchise. That's probably the reason why mainline games have stayed on the handheld. I'm sure Nintendo would put Pokemon on consoles if they could.

exactly

Game Freak has always said Pokemon will stay on handhelds because it's the sense of those pocket monsters after all. We might never see a proper home console Pokemon game.
Just like we will never see a Pokemon game in which you can collect them all.

In my opinion this is an issue about game quality. I'm usually a pretty good sales indicator (I buy it - the market is all over it. I hate it - the market hates it too) and since 2010 the quality of Nintendo's software output just keeps decreasing. Zelda, Mario, Nintendoland, Pikmin - I was disappointed with all of these games (compared to their predecessors).

The last time this happened was during the Gamecube era when Nintendo forced developers to release games within 1 year. Right now (and I can't believe no one mentions this) it's because Nintendo underestimated the resources needed to develop HD games and their big internal restructuring (new hq, etc.). It so reminds me of the Gamecube days it's not even funny.