The DOJ in building its case against the deal includes projections from American's standalone reorganization proposal, which was built as a rival to US Airways' overtures. Vaughn Cordle, a partner at Ionosphere Capital LLC, said that relying on those rosy forecasts is a mistake.

"No serious analyst believed American's former executives when they said they would aggressively grow their key hubs after they emerged from bankruptcy as an independent airline," Cordle wrote. "It was a narrative designed to help the American CEO and core team remain in control and also placate various stakeholders, especially labor."

If American is forced to go it alone and does expand as planned, Cordle said that the growth would destroy shareholder value which in turn would force management to reverse course.

"Hence this growth story was pure fantasy; a fantasy that the DOJ now ironically uses as their own evidence that the airline could remain viable and strong as an independent airline," he said.

All in, analysts have concluded that either by settlement or after victory in court the deal is likely to be consummated, with a settlement seemingly more palatable to regulators.

"We think there is still an excellent chance this case never goes to trial since it can and should be resolved with a negotiated settlement, but if it does we expect the airlines to prevail," Vicki Bryan, a senior high-yield analyst at Gimme Credit LLC, said in a recent note.

But a number of antitrust practitioners take the opposite view -- that there is no way this case doesn't go to trial.

If there is a settlement, the agreement will likely only address DOJ concerns that are easily addressed, such as concentration at Reagan National Airport or reduced competition along specific routes, which could be fixed by divestitures to other airlines.

From the airlines' court filings, in fact, it appears they tried to do just that. While antitrust sources said that a settlement on those issues is still possible, such a move would serve only to narrow the issues at trials. There is not obvious settlement for the DOJ's conviction that eliminating US Airways and American as separate network carriers would harm competition and that US Airways has a unique hub system that makes it a disruptive player in the market.

If you liked this article you might like

Cramer: Wall Street's Game du Jour, Leapfrogging

Halliburton-Baker Hughes Merger Has Fair Shot at Regulatory Approval

Donald Trump: 'I Ran a Great Airline.'

Jim Cramer's Take on Comcast's Dead Merger Deal With Time Warner Cable

One Reason American Airlines (AAL) Stock Is Up Today