This whole discussion is quite frankly a waste of time. UA has decided, for whatever reason, that it needs to schedule a longer amount of time for that flight. Telling them that it is "illogical" for them to schedule the way they did will not result in a schedule change which will allow your connection to work.

As far as afternoon congestion into EWR, note that smaller planes (and certain UX carriers) are far more likely to be delayed. It seems like there is a ground stop program almost every afternoon into EWR, so padding the schedules like crazy is probably wise.