I think this new monetization was brought in by the new president of Nintendo. He made it clear when he started that he is not happy with how profitable the mobile division is. I think this is one of the changes he made was to try out the subscription model. For who gets to make the decisions, on a free to pay mobile game, its up to the developers to make a game that will make the company money while being free.If they aren't doing that, a publisher must step in to change that. Unless the goal is not to make loads of cash.
For Niatic, thats a bit of a different situation. They have I think a ton of freedom to do what they want. And why shouldn't they, they madea great product that is bringing bucket loads of cash.
Personally, I hate the way I am seeing Nintendo go with these subscription models.