Considered the freeway capital of the world, it wasn't always that way. California's State Highway System dates back to 1895 when the state took control of the Lake Tahoe Wagon Rd (part of modern US 50). The State Highway Bond Act of 1909, the first of many, allocated $18 million dollars to adopt 3000 miles in the state. These routes were assigned numbers legislatively, starting from one. The Automobile Club of Southern California (ACSC) elected to take charge in signing routes, starting with route that were certified and adopted by the Federal Government for the US Highway System in 1926. It then only made sense to sign state routes as well, but instead of signing the legislative numbers, the ACSC assigned more cohesive numbers. One numerical signed route may be overlaid upon multiple Legislative Route Numbers (LRNs). They tried to keep as many Signed State Routes (SSRs) true to the LRN, but in some cases this was not possible.
This led to a very convoluted system. California, the Federal Government, and ACSC started overlapping many routes. While it may make sense to 'multiplex' two numbers, maybe even three, for a few dozen miles, many ran for hundreds of miles. US 70 in California, for instance, never made a break from US 60 or US 99 and was always co-routed. US 91 was extended from Barstow to Long Beach via US 66, US 395 and SSR 18. Consistency may make sense for out of state travelers, but control cities, directional tabs among other telling signs should have been enough to get you on the right road.
Confusion ensued into the freeway era. Freeways were given names to help reduce the issue, and were signed as such. Many freeways may still be signed with their route numbers nowadays, but this has fallen out of popularity with Caltrans. Most were named with cities they began, ended in, or passed through (i.e., The San Bernardino Freeway, The Santa Monica Freeway, The Hollywood Freeway), although some were given broad names (The Golden State Highway/Freeway). This worked for a while until California could come up with a better system.
In 1964, California adopted the Great Renumbering plan, setting forth the notion of 'One Road, One Number'. This killed most of multiplexes, but favored the newer high-speed Interstate routes over the older US Highway routes. This led to the removal of many historic routes, like US 66 and US 99, the truncation of US 101 and US 6, as well as the removal of all US Alternative routes. Some sections of routes retained their US Highways Number but were demoted to State Routes, like SR 99 (US 99) and SR 60 (US 60). This was due to the fact that many routes no longer reached the standards of the US Highway System, which was that the route had to be inter-state. That is the reason why US 101 kept it's designation as a US Highway. SR 99 is eligible to be re-adopted into the US Highway System, but Caltrans decided to favor I-5 and make sure people knew that was the main route instead of the 99.
Most routes kept their old designation while new super-highways were being built, like US 66 and I-40. Many retained both their new and old shields while people got used to the new numbers, but some were shocked to find all the other routes gone. It's worth noting that the Interstate system predated the renumbering by 6 years, allowing most people to become familiar with the route numbers. Most still relied on the given name of the freeway for a full generation.