Eh Nintendo may not be encouraging them as far as we know, but they aren't stopping them either by having them delay the game like all their other developers are willing to do. Naturally they stand to gain more profits with Game Freak putting in the bare minimum resources.
I'm not sure what's Nintendo's role in all of this. On one hand, the weakening of the pokemon games from GameFreak's grasp could give Nintendo the opportunity to exert more control over the franchise, and thus its incredibly profitable side businesses. On the other hand, the mobile-ization of the series is just what Nintendo needs the absolute least, considering it still is their biggest hardware seller.
The general ownership of the IP is an overall headache, and I assume Game Freak is being pulled between The Pokemon Co. and Nintendo, with added problems of leadership, work overload, team morale and really tight deadlines. Mobile profits being as high as they are is in no way helping Game Freak in getting their shit together, considering the impossible task of keeping up with microtransaction money.
You know it deserves the GOTY.