The FAA has returned the $6.6 billion plan to the city. FAA spokesman Tony Molinaro says he expects the city to analyze the comments, make changes and resubmit the airport layout document to the agency.
He says that without the changes, the plan would not produce the suggested 95 percent reduction in flight delays during bad weather.
The agency also suggests that adding a diagonal runway to the airport's south end could help the airport move airplanes better.
City officials disagree, saying the asserted benefits do not withstand analysis.