While God does love Nineveh and desires that all the people
there turn from their wicked ways, in this story, God is working with another purpose in mind, and to reach that purpose, He wanted the whole wicked city of Nineveh to repent.
2 Chronicles 7:13 - 14 - If I shut up heaven that
there be no rain, or if I command the locusts to devour the land, or if I send pestilence among my people; If my people, which are called by my name, shall humble themselves, and pray, and seek my face, and
turn from their
wicked ways; then will I hear
from heaven, and will forgive their sin, and will heal their land.