All of this is just business and can be messy, especially when you're talking about youth sports (read cottage industry).
While I fully understand all the arguments about development style, philosophy and building the best club and so on, at the end of the day its all about dollars. The control issue being implied is more of business control rather than soccer control.
Couple of things to think about. Sotilo is owned by Estillo-Honda and has academies all over the world as well as own couple of professional teams in Scandinavia and Africa. They also took a small stake in Surf Sports (parent company for Surf SC) few years ago. When they announced LA Surf, it make sense from branding but probably never realized what they expected so why not go back to being Sotilo and grow their own brand. As for SGV, probably didn't like the arrangement so why not join Soltilo. Sounds like they have been a gypsy club the last few years.
We tend to think that club soccer is youth sports first, then business but in reality, its business first and youth soccer is the medium in which the money flows. Its all about branding and marketing. Kids are commodity that funnels monies to the club from parents (consumer).
May not like it but its true...
My kids played with (and I served in various BOD roles with) a community-based non-profit youth sports club, so I can attest that it is not all about mining money from eager parents.
However, the "it's just a business" theory would explain some of the interactions we had with other clubs.