Wikipedia doesn't give much mention to the history of US 90's routing, but I saw this intriguing 1949 Houston map at TexasFreeway.com:
(https://www.aaroads.com/forum/proxy.php?request=http%3A%2F%2Fwww.texasfreeway.com%2Fhouston%2Fhistoric%2Ffreeway_planning_maps%2Fimages%2F1949_freeway_map_medres.jpg&hash=f69bda4e27e85e16bcab57e736cd08dd4b15a855)
Beyond the fact that it shows a lot of the still-existing state route numbers (225, 288, 35) in the area, it specifically labels what was then US 59 (and is now US 90 Alternate) as "Old US 90."
I had always assumed the Katy Road routing, being the most direct pathway west, was US 90 from the start...but if it wasn't, when did it become the US 90 mainline, with the southern routing between east Houston and Seguin becoming Alternate US 90? In 1935, the Old Spanish Trail/South Main Street southern corridor was still US 90:
http://mappery.com/map-of/Antique-map-of-Houston-from-1935