The city asked for an upper-level public observatory. Millennium Partners proposed a ground-level Great Hall instead.

As the Boston Planning and Development Agency moves to the next step in its review of the controversial project on the Winthrop Square garage site at 115 Federal St., it’s indicating skepticism about whether the 12,740-square-foot public hall running between Federal and Devonshire streets would provide sufficient public amenities.

“As currently designed, the Great Hall space resembles a transit hub, but absent any transit connections,” the agency stated in a scoping determination released this week. “Retail uses alone do not achieve the distinction of a great civic amenity.”

The agency suggested that Millennium reconsider the idea of a high-level “public or quasi-public” observatory. The document lists issues that Millennium should address as part of the agency’s project review.

Millennium executives said the Great Hall will form a new pedestrian connection between the Financial District and Downtown Crossing, and be suitable for public events ranging from fashion shows and farmers’ markets to art exhibits and the mayor’s State of the City address. But the BPDA raised concerns about Millennium’s emphasis on seasonal programming and lack of specifics about who would be responsible for coordinating events.

“In addition, it is unclear how the programming might enhance or detract from similar outdoor activities on the Summer Street mall in Downtown Crossing or on Dewey Square near South Station,” the document states. Those activities are coordinated by the Downtown Boston Business Improvement District and the Rose Kennedy Greenway Conservancy.

The project including luxury condos and commercial space already faces a pair of hurdles at the Boston city council and state Legislature, which will review a proposed Home Rule petition exempting the tower from state laws limiting shadow on the Boston Common and Public Garden from new development.

And Massport has warned that the height of the 775-foot-tall tower would interfere with Logan International Airport’s airspace and shift more departures from runway 27 over South Boston to runway 33L, which sends air traffic over the cities of Chelsea and Somerville.