Well, if you put it in perspective, the whole Pokemon universe was created by one single Pokemon (or at least, we know there's an "Alpha" Pokemon). That Pokemon created all the ecosystem on earth by creating another powerful beings. Some that could control the time and space itself. Others were in charge of the elements and shaped the earth to the point of being inhabitable. Guardians to protect and regain the world balance. One that was in charge of the creation of all the other Pokemon.
That alpha Pokemon also created three other Pokemon in order to give life to the humanity. These Pokemon represented, the spirit, wisdom, and desire. (and there are more, like the one that origin dreams, and the other one that origin nightmares)
No God or demi-God Pokemon is intangible in this verse, although some are so strong they can rip off time and space or create their own parallel worlds. And all the gods known in this universe cohabit in the same time as humans.
So, with these Gods wandering around, keeping the balance of the earth and shaping it, you would think that they actually want this system to work. On earth and in another planets, as there's also Pokemon able to travel in the space.
So there's your deus ex machina. God is the answer.
p.s: It's all made for good and fun. Stop overthinking about this. :p
