Part of it is the lack of a West Coast hub. Once they integrate the two carriers, they'll be able to build more efficiency into the schedule.

Right now, the 12:30 p.m. arrivals wouldn't leave until say 1:30 p.m., which make it to IAH or EWR too late for many connections (EWR especially).

The turns on the late night flights are really obnoxious and are textbook CO -- they probably fly the crew EWR-PDX-IAH or IAH-PDX-EWR without an overnight, so even though there are planes there, there are no valid crew to fly them. Later flights are more prone to delays than earlier flights, subjecting the redeyes to more possible delays. At least PDX is not a delay-prone city. It's really frustrating when they schedule like that in SFO in the rainy season. But at least they save some hotel rooms.