“It just seems if we are investing a billion in station upgrades we think that some of those stations should get elevators,” said Polly Trottenberg, the commissioner of the city’s Department of Transportation. “I don’t understand nonetheless how they reached the decision, picking some of these stations.”

But Mr. Cuomo and transit officials have argued that improving the appearance of stations is part of improving the experience for riders and that the system is already undergoing a major face-lift as part of the subway emergency plan that was begun last summer.

At Thursday’s meeting, Andy Byford, the president of New York City Transit, the M.T.A.’s subway division, offered a full-throated endorsement of Mr. Cuomo’s plan, arguing that some of the work addressed structural issues that could no longer be ignored. “If they were purely cosmetic then I would have a problem with it,” Mr. Byford said.

Mr. Byford said he had spent weeks analyzing the stations slated to be enhanced and had come to understand why things like elevators were not part of the plan, explaining that some of the stations were close to accessible stations, while in other cases figuring out how to make a station compliant with the Americans with Disabilities Act would drag out the necessary work.

“To wait for perfection at every station?’’ he said.“Some will fall into a dangerous state of disrepair, and you will fall into my scenario of, ‘yes it’s ADA-compliant but oops’” — the station would be inaccessible because it had fallen apart.