Darn, looks like SFO-LAX-EWR actually gets FEWER miles than SFO-IAH-EWR. And the flight from IAH-EWR is probably the first of the day. Only way I'd want to take a SFO-EWR direct flight is if I got rebooked into Y/B for 150% mileage. And the thought of leaving SFO earlier the day before and spending the night at IAH doesn't appeal to me either.
Of course, I'd be willing to take SFO-HNL-LAX-EWR as an alternative, but I don't think UA will let me have that