Yes, that's the best they can do, but it's partially because of the merger (using the pre-merger UA gates in Terminal A, those are the "teen" gates), and partially because of the terrible layout of Terminal A, which requires you to go through security separately for every pod at Terminal A...
Unless there is a major renovation of Terminal A, really the only solution in the short term would be for UaCo to reduce the number of flights it operates out of EWR.