Years ago, they definitely buffered in longer times to the officially scheduled departure/arrival times to avoid those nasty fines the F.A.A./D.O.T. were giving them, saying a flight from MIA to ORD was 3 Hrs 25 mins when flying time was more like 2 hrs 30 mins.
I've worked on many logistics projects (not aviation based but definitely large scale transport/finite space based) all with their own blend of unique problems. I would be curious if we have any aviation based logistics experts who can tell is it just the lack of gates (60 + E terminal overflow) or is it the gate/baggage handling management.