At the top of his change, Mr. O’Neill said he would name Chief Terence A. Monahan as the department’s highest-ranking uniformed officer, the chief of department, and would promote Assistant Chief Rodney Harrison to fill Chief Monahan’s spot as chief of patrol. Both men have been overseeing the neighborhood policing efforts and consider it a philosophy for policing, more than simply an experiment.

Chief Monahan has been a senior commander for more than a decade, and his performance during the police response to protests at the 2004 Republican National Convention prompted a lawsuit by the New York Civil Liberties Union and was later sharply criticized by the city’s Civilian Complaint Review Board.

Andrew Case, a lawyer who was a spokesman for the review board at the time, recalled on Monday that then-Assistant Chief Monahan ordered 227 arrests of people on Aug. 31, 2004, but that all of the cases were later “dismissed” by the Manhattan district attorney’s office.

The agency’s “investigation showed that Monahan ordered the crowd to disperse while they were pinned in by a fence on one side and a line of officers on the other,” Mr. Case said. “In today’s political climate, it is particularly troubling that someone who supervised the arrest of hundreds of peaceful demonstrators has been promoted to the department’s top uniform position.”

And, for all of Mr. O’Neill’s moves, none of them represent a dramatic break from Mr. Bratton’s vision, as Mr. O’Neill is still surrounded by many of the same top aides and deputy commissioners that the former commissioner had put in place, particularly Dermot Shea, the department’s chief of crime control strategies, and Lawrence Byrne, its top legal official.

Still, such moves are not uncommon within the city police agency, the nation’s largest, when a new leader seeks to brand it with transformative change or, perhaps, settle old scores. When Mr. Bratton became commissioner the first time, in 1994, he ushered in a phalanx of young “super chiefs” and carried out a smaller shake-up when he took over a second time in 2014. Patrick V. Murphy, who became police commissioner in 1970, began his tenure by asking top commanders, “What is your intention?” recalled Robert J. Louden, a New York police officer from 1966 to 1987 who is professor emeritus of criminal justice at Georgian Court University, in New Jersey.

By contrast, Mr. O’Neill moved slowly in moving those in ranks below him. He could have acted in September 2016, when he succeeded Mr. Bratton, rather than awaiting the election’s outcome. “But he took his time, and watched as neighborhood policing evolved, and the result is the lowest homicide rate, lowest shooting rate and pushing toward community confidence,” said Chuck Wexler, the head of the Police Executive Research Forum, a Washington think tank.