All of the above gets more interesting as more of the historic information come to light. In many ways, cities knew that being on a signed US route would be "good for business" and thus encouraged the routings to come their way. (The Santa Monica saga that you allude to comes to mind as a good example.)
One really interesting thing about much of this is that what was good for Santa Monica (and perhaps Hollywood) would be terrible for Downtown Los Angeles. A 66 routing from Pasadena to Fletcher/San Fernando would overshoot Downtown LA and would mean a significant amount of backtracking for any travel between Pasadena and Downtown LA. Fair Oaks/Huntington or Pasadena Ave (the part of Figueroa in Eagle Rock was once part of Pasadena Ave and the roadway led to Broadway before the completion of the Figueroa street tunnels) would still be the main ways of connecting Pasadena to LA, and each had some history of being a 66 routing. Who would possibly use Fletcher to get from Pasadena to Downtown LA?
When designing any new routing, particularly in an urban environment where several main streets were already laid out, one has to decide what areas will be connected and what areas will be bypassed. This is all the more true when discussion of rerouting is also at play. Coming in from Arcadia, one could bypass Pasadena by taking Huntington or connect to Pasadena by staying on a Foothill or Colorado routing. From Pasadena, once could bypass LA by taking Fletcher or connect to LA via Pasadena Ave or Fair Oaks. The above saga seems to indicate that AASHO was strongly against bypassing LA, because that was the key destination for the western end of US 66. People were headed to LA not merely the Pacific Ocean. US 66 could be extended to Santa Monica (and it eventually was) but not at the expense of LA.
For 99, LA was not the terminus, but still an important route along the way. Connecting from San Fernando (and the Central Valley) to San Bernardino (and the Desert areas on the way to Calexico) would add a lot of distance if 99 were routed through LA. So long as 99 ran along the 66-Foothill route, 99 avoided central LA. It was only the introduction of Aliso-Garvey as a primary route to the east that allowed for a retoute of 99 to better serve central LA. FWIW, it seems that in AASHO's eyes, Downtown LA was negotiable for 99, but critical for 66. So while Fletcher was signed for 66 for a few years, it didn't remain there for long.