To a point I understand why it all was done this the way it was but man. If i could redesign the ATL airport two big things I would do....

SkyClubs. One center large club in the middle and a club on each end of the concourse that are slightly smaller. Think DTW A.
tunnels. In addition to the main tunnel with the plane train, smaller tunnels at each end that just have moving walk ways.

I think both would help with some of ATL's biggest issues (SkyClub capacity and plane train capacity.) Plus make some connection options much shorter thus making the hub run more smoothly.

Other thing I would love to fix but I'm not sure how to realistically do so, bigger gate areas and more room to walk. Only thing I could think of is go the old shopping mall method. Put all the restaurants and shops on a second floor but I don't know if that would really be feasible.