CO does the same thing on connecting flights - making for example DCA-EWR-LAX cheaper than DCA-IAH-LAX - trying force you to the EWR connection.

The EWR connection earns more miles, but you are having to connect in EWR with all its problems. Flights into IAH do not have all the delay problems. I will take the fewer miles to split the trip in half and have a better change of connecting on time. CO - stop forcing EWR connections as cheaper flights - instead reduce the number of flights into EWR.