That Manaphy is able to take human form, or even to copy a specific human, is not particularly unusual; this ability is documented among the gods in Latias and Mew, and is likely shared by others as well. But Manaphy transforms not by copying, but by quite literally swapping their consciousness with another living thing. Being chosen as Manaphy's disguise is the only known way for humans to inhabit a pokemon body, and those who have experienced it have found it a fascinating opportunity for both understanding the natural world and briefly obtaining unparalleled power.
Manaphy is a god of water, and its body contains a remarkable ability to manipulate anything composed of water vapor or liquid water, from clouds to the entire ocean. When gifted with this power, those whose hearts are swapped with Manaphy quickly take advantage of the abilities of their borrowed form. Some do so benevolently, putting on beautiful displays of pokemon-shaped clouds or carrying rain and irrigation to where it is desperately needed, but even they often cause tragedy when they find the world's water difficult to control.
But water can be an extremely destructive force, and there are countless individuals who would use the power of the gods for vengeance. Flash floods and tsunamis abound when Manaphy swaps hearts with the wrong human, and many bizarre reports single individuals being targeted by massive storms, waves, or even hands of water reaching up from lakes or rivers also correlate with these periods. Perhaps it is best that only pokemon – even a spiteful and occasionally violent one like Manaphy – are given the power of the divine, for humanity can not be trusted with such awesome power.