The Second Avenue subway, finally under construction on the Upper East Side of Manhattan,  is of course a vast  underground project. The $4.45 billion first  phase, now scheduled to be completed in 2018, will extend from 96th  Street  to 63rd Street and Lexington  Avenue.  
  But the project will also include construction above ground — not just  station entrances but also a half-dozen boxy buildings on corners along  Second Avenue that the transit agency acquired through condemnation.      These so-called ancillary buildings, ranging in height from five to  eight stories, will house ventilation equipment. They are also intended  to disperse smoke and allow for evacuation  from subway tunnels in the  event of an emergency.  
  To the Metropolitan Transportation Authority of New York, the proposed buildings, designed by DMJM+Harris and Arup,  part of the team that designed the Jet Blue Terminal at Kennedy   International Airport, are “handsome in proportion and detail, while simple and straightforward in design.”  
  But to some real estate specialists, the structures represent a missed  opportunity or an unwelcome industrial intrusion into a residential  neighborhood, or both. Richard Bass,  the chief planning and development  specialist for Herrick, Feinstein, a law firm based in Midtown  Manhattan, said that at three of the sites — on 97th Street, 72nd Street  and 69th Street — the M.T.A. could have worked with private developers to incorporate the ancillary buildings into residential towers.  
  Mr. Bass represented a co-op on 69th Street in negotiations with the  M.T.A. over the adjacent ancillary building. He is not involved in a  lawsuit the co-op filed against the Federal Transit Administration and  the M.T.A.  
  On each of the corners cited by Mr. Bass, the developers could have  sought development rights, known as air rights, from smaller adjacent  residential buildings, Mr. Bass said. He said taller apartment buildings  would have been more in character with a residential neighborhood and  would have helped fill a need for moderately priced housing. In  addition, the M.T.A. could have had the developers  share in the cost of  the subway structures, Mr. Bass said.  
  “It seems that the M.T.A. missed an opportunity to play in  the real  estate game in a way that would have been a win-win-win,”  Mr. Bass  said. “This could have provided the M.T.A. with a more cost-effective  facility,    a more urbanistically appropriate structure for the  surrounding  community,   and an opportunity to create more housing in  partnership with developers.”  
  Citing the pending lawsuit filed by the 69th Street co-op, M.T.A.  officials were unwilling to be interviewed. But they did agree to answer  written questions by e-mail.  They said they would not release cost  estimates for the ancillary buildings until they had hired the  contractors. Nor would they say how much they had paid for the building  sites.  
  Kevin Ortiz, an M.T.A. spokesman, said by e-mail that the agency had  worked with developers on both the 97th Street site, where the Century  Lumber Corporation once stood, and on 72nd Street, the longtime home of  Falk Drug and Surgical Supplies. Plans for 72nd Street, where the site  measures 75 feet by 75 feet, were scuttled because “in order for a  development to work, additional property would have had to be acquired,  which we couldn’t justify as a transportation use,” he said.  
  On 97th Street, “M.T.A. Real Estate worked very long and hard to make it  work, but in the end the developer lost interest,” he said.  
  In a subsequent e-mail, Aaron Donovan, another M.T.A. spokesman, said  the developers that the agency had consulted owned the sites. Mr.  Donovan said the agency had not issued requests for proposals from  developers “because we didn’t own the properties,” which were  acquired  through eminent domain.  
  According to the M.T.A., only the 97th Street site, which measures 100  feet by 125 feet, is large enough to accommodate a residential  development. The M.T.A. also would not say why it did not consult a  second developer for that site.  
  Several  developers, architects and engineers took issue with the M.T.A.  and said the agency should have sought to work with private developers.  “It does sound like a missed opportunity,” said Douglas Durst, who developed the Bank of America  building at One Bryant Park. The 69th Street site, at 50 feet by 80  feet, “is a little tight,” he said, “but the others are the perfect size  for residential.”  
  Some real estate specialists said the transit agency could have found a  model in an agreement struck in connection with the extension of the No.  7 subway line on the far West Side of Manhattan.  
  On a large site at 26th Street and 11th Avenue owned by the Moinian  Group, the M.T.A. plans to build a seven-story ancillary structure for  that line. The building was designed so  Moinian Group could eventually  build a residential tower that would incorporate the M.T.A. building,  said Oskar Brecher, director of development for Moinian.  
  “It was a very complicated process that required a great deal of time,”  Mr. Brecher said. “The midwife was the Hudson Yards Development  Corporation,”  he added, referring to the city agency overseeing the  development of the area.  
  Around the country, public officials have worked with the private sector  to encourage development along new mass transit lines to increase  ridership.  Of course, no one thinks  the Second Avenue subway will lack  riders.  
  But transit-oriented developments can also be used to defray  construction costs. Julia Vitullo-Martin, director of the Center for  Urban Innovation at the Regional Plan Association,  said the M.T.A. typically had not engaged in strategic thinking when it  came to its real estate. “The M.T.A. does not think of its real estate  as either an investment opportunity or a development opportunity,” she  said.  
  For Civitas, a civic group  representing the Upper East Side and East Harlem, the critical issue is  how  the buildings, to be made of terra cotta tile, glass and granite,  will affect street life along Second Avenue. The local community board  has yet to take a formal position on the ancillary buildings.  
  “Certainly, the design of these structures could be improved,” said  Hunter Armstrong, the executive director. “Having large blank industrial  buildings inserted into a lively streetscape will diminish the activity  and appeal of Second Avenue,” he said. Civitas persuaded the M.T.A. to  include retail spaces in two of the sites — 360 square feet at 69th  Street and 240 square feet at 72nd Street.  
  Mr. Ortiz said the M.T.A. chose this style so that the public would  recognize the buildings as industrial. He said the structures were not  intended to be “starchitecture” but would be “respectful of their  immediate surroundings.”  The building materials “need to be robust,” he  said, “as they will receive only very minimal maintenance attention.”  
  The M.T.A. did not always intend to make the buildings look industrial.  In the final environmental impact statement, completed in 2004, it said  they “could be designed to appear like a neighborhood row house in  height, scale, materials and colors.”  
  The M.T.A.’s decision to build industrial rather than brownstonelike  buildings was cited in a federal lawsuit filed in January against the  Federal Transit Administration and the M.T.A. by  a cooperative  apartment building, 233 East 69th Street. Residents say that, as  now  conceived, the auxiliary building would be so close to their  building  that 32 windows facing east would be blocked. They also contend that the  building “would be totally out of harmony” with the neighborhood.  
  At a conference on  April 14, the M.T.A. argued that its building would  blend in with the surroundings, but  Judge William H. Pauley III of   Federal District Court in Manhattan disagreed. “You’re asking me to  suspend my common sense,” he said.  
  The M.T.A. had no comment on the lawsuit, which is still in its early stages.