As usual, things are more complicated than your analysis.
2 pilots vs 4?
Well, a 737 crew do a SYD-MEL-SYD pattern they are paid 3 hours. 787 crew do it and they get 5:30 and the 787 hourly rate is higher. So from a pilot cost perspective is it cheaper running 2 737’s?
Obviously the 787 looks better if they do another return service but you’ll be outside the peak time by then so do you need to fly a widebody load then?
If less than 100% load factor is achieved on the 738...
Well that is surely a situation where 2 737’s are a significant advantage. Look at how Qantas dynamically manage capacity during the peak hours each day. On days with a light load they cancel the half-past the hour flight and roll pax onto the on the hour flight. Huge cost saving for the company.
You can’t do that with a half empty 787 as you’d end up with an hour long hole in the schedule and business passengers won’t stand for it.
Gate congestion?
How many gates in SYD, MEL and BNE can 787’s park on? A quarter, a third, of the available gates?? If you widen the gates you end up with fewer anyway.
And what of the cost of the aircraft? The 789 costs almost triple the price of a 738 yet holds less than double the passengers.
The 789 is a brilliant aircraft and I hope they order many more but to say that they are foolish for not running them SYD-MEL ignores a lot of the real operating dynamics of that route.