I've read the complaint now, and here are a couple (brief) reactions, which should be used for discussion purposes only. These aren't legal advice (duh), I'm not involved in this matter (duh, I wouldn't be posting If I was), but I am an antitrust lawyer, so I hope my views can get the discussion a bit more focused.
1) The big shift here is the emphasis on connecting service as a discipline on prices for nonstops. In fact, the city-pair market definitions are obviously calculated as connecting, not just non-stop. See Appendix A to the Complaint. This is diametrically opposed to anything the regulators have done before.
2) The Complaint talks out of both sides of its both about B6 and WN as competitive constraints on the legacies. On one hand, the Complaint seeks to paint them as offering limited competitive discipline because they don't have the efficiencies of a true hub and spoke system, but on the other they credit B6 discipline on nonstop routes at DCA and include them in pricing comparisons. (To be fair, it seems that the parties' documents treated them about the same.)
3) Same double-speak exists about US' Advance Fares pricing on connecting routes. The Complaint claims in once place that other legacies hate this pricing and don't do it themselves, but then in another cites an example of them doing just so.
4) These parties brought this suit on themselves. I obviously can't see the documents themselves, but their executives, particularly US', wrote some monstrously stupid things in emails, at least from an antitrust perspective. This complaint practically wrote itself. In fact, the connecting competition argument is practically just stitching together emails from Parker and a couple other US folks. I'm sure there's probably context to explain them, but those quotes look awful.
5) As expected, it makes a big deal out of DCA, but DCA is by no means the only problem here. DOJ's concerns will not be assuaged only with a slot divestiture at DCA.
6) The carriers also brought upon themselves a strong argument regarding coordinated interaction post-merger. To be clear, conscious parallelism isn't illegal, but it does cost consumers money and it's a valid reason for DOJ to want to block the merger. The Complaint cites bag fees, change fees, and inflight service as examples, but also fares filed through ATPCO.
7) DOJ seems to believe post-bankruptcy AA can and will be a viable competitor.
I've seen a lot of merger injunction complaints, both of the negotiating ploy variety and the "we-mean-business" variety. This one's the latter. DOJ really threw the kitchen sink at this one and it sure looks like they really do mean to block it.