I've got a couple guesses, and maybe one of the Champs will chime in with a better explanation.
For reference I searched on Google for the directions from those to locations, and the route Waze uses was one of the 3 options that Google gave, and Google gave all 3 about the same amount of travel time.
So it may be, with the speed data that Waze has, it feels taking the highways is the quicker route.
Do you have "shortest route" selected in the client under navigation? Not sure how well that works, I know I've seen UR's complaining that Waze isn't actually giving shortest route directions.
Another issue may be the distance between those locations. Waze prefers highways for long distance travel, so since all those roads are streets or primary streets, Waze might be ignoring them.
It also might be a good idea to go over the route manually in the editor, and see if you can find any disconnections or improper turn restrictions which might be keeping Waze from routing over them.
California, USA - OC/LA/SB/Riverside Area Manager