Having traveled both routes by car numerous times, the Natron Cutoff is a far superior route compared with the Siskiyou route based on topography. The geologic forces created grand lava flows which produced relatively flat plateau like topography in central southern Oregon compared with the island arc features of southwest Oregon which is characterized by steep sloped mountains with narrow and winding canyons.

I suspect the initial draw to build the Siskiyou Route was to help exploit the vast timber resources located in southwestern Oregon. As time went on, a more efficient route became desirable, thus the evolution of the Natron Cutoff. If I remember my rail history, the Natron Cutoff was originally part of a scheme to build a railroad across central Oregon from Eugene to Burns to tie in with the Oregon Short Line on the Idaho border.