It has been a difficult two weeks for Alaska Airlines' (ALK - Get Report) proposed acquisition of Virgin America (VA .

While airline executives have repeatedly made the case that the deal is on track and that combining the two carriers into one with 7% of all U.S. passengers would benefit consumers, investors recently have expressed doubts regarding the final configuration of the merged carrier.

Alaska's offering price for Virgin America shares is $57, but shares closed Friday at $52.95.

On April 1, the day before the deal was announced, Virgin America shares closed at $38.90. On the next trading day, they closed at $55.11. On July 5, they reached a 2016 high of $56.64.

On Sept. 22, shares dipped 5% to $53.20 after reports surfaced that airline executives had met with officials from the U.S. Department of Justice's antitrust division, an indication that the acquisition might not be approved by a Sept. 30 target date.

And on Sept. 26, Alaska and Virgin extended that date, saying they would not consummate the deal before Oct. 17 unless DOJ approves it before then.

"The extension gives the DOJ additional time to review the proposed merger," the two carriers said. "The two airlines are confident they will address any concerns and obtain regulatory approval."

The merger will allow "for more robust competition against the big four airlines, which control 84% of the domestic market," they said.

Tod Northman, an aviation attorney for Tucker Ellis in Cleveland, said he believes the deal will be approved because it represents a step in the creation of a fifth national airline.

But "if you look at this from the West Coast perspective, {the Justice Department} would like to see Virgin America be a competitor to Alaska," he said.

"From a national perspective I love {the deal}," Northman said. "From a regional perspective, I understand the concerns."

New concerns emerged last week in a report by Piper Jaffray analyst Alex Olvera, who analyzed the merger in terms of code share flights that American Airlines (AAL - Get Report) operates in partnership with Alaska. Code shares enable airlines to sell tickets on one another's flights.

American and Alaska code share on eight of the 11 flights where Alaska and Virgin America both fly, Olvera said.

"Our analysis leads us to believe that this merger is likely to result in higher ticket prices {and} less choice for consumers and it is likely to remove capacity in hub to city and hub to hub non-stop routes," he said.

Olvera acknowledged that people in the airline industry, whom he interviewed, "believe the merger is likely to receive DOJ clearance." But his view is that "the risk of a DOJ suit to block the deal is high" due to the code shares.

Alaska and Virgin America overlap on non-stop flights in 11 city pairs.

From San Francisco, both fly to Palm Springs, Portland, Chicago, Seattle, JFK and Los Angeles. American and Alaska code share on flights to Portland, Seattle, JFK and Los Angeles; a merger would make new Alaska the biggest carrier to all four cities.

From Los Angeles, Alaska and Virgin America both fly to JFK, Honolulu, Boston, Chicago and Seattle. American and Alaska code share on flights to JFK, Honolulu, Boston and Chicago. A merger would make new Alaska the biggest on JFK, Honolulu, Boston and Seattle.

Alaska/Virgin America is the first airline merger overseen by Renata Hesse, a graduate of the University of California, Berkeley, School of Law, who took over as head of the antitrust division in April.

"I think Justice is going to want to put their fingerprints on this" by requiring divestitures, Northman said.

Aviation consultant Robert Mann agreed, saying, "I think the effort underway now is for Alaska to identify something that looks attractive to DOJ as a concession but which really doesn't have commensurate value to Alaska," he said.

One possibility is for Virgin America to give up its slots at Dallas's Love Field, where it began flying in October 2014. Mann has long felt that the airline gains little from its effort to compete at an airport where Southwest has a 91% market share.

However, it may be that "DOJ looks at Virgin America in Love Field as providing price discipline in the market, even though it's actually just a competitive failure," Mann said. "Maybe Alaska could do a better job."

Another possibility is for DOJ to increase access for other carriers at Washington Reagan National Airport, its hometown airport, where both Virgin America and Alaska have slots. "DOJ can look at these and decide which is least essential," Mann said.

Mann said it's important for DOJ to consider that for all of its recent success, Virgin America is not necessarily an airline that could prosper indefinitely were fuel prices to rise and the tech boom that powers the San Francisco economy to slow.

The carrier has about half its capacity at San Francisco International Airport.

The tech industry is cyclical, Mann noted, adding, "When Silicon Valley implodes and you can rent an apartment in San Francisco, Virgin America is going to have problems."

This article is commentary by an independent contributor. At the time of publication, the author held no positions in the stocks mentioned.