She just wasn't a good fit for the administration temperamentally and eventually found herself frozen out and with zero influence
Good riddance to Nikki Haley, the soon-departed UN Ambassador. Ignore most of the speculation about her grand future plans to run for President or take Lindsey Graham's Senate seat if Trump dumps Jeff Sessions and replaces him with the South Carolina Senator.
The simple explanation that often is the most sensible is that Haley's influence with the President had reached near zero. She was iced out by her ideological ally John Bolton and by Secretary of State Mike Pompeo.
She had no future inside the Trump Administration, having angered the President a few times and tried to grab the spotlight even more often.
Trump's UN General Assembly performance was another point of upset for Haley--further indication how far outside the loop she had descended.
It was just time to go. Smart move for someone as ambitious as she is. For some, New York City is Siberia when all the action is in the immediate vicinity of the Oval Office.
Source: Sic Semper Tyrannis