Someone like Chad "Scizor" H. or a POP person could answer this better, but I'll supply a possible one, since I'm always discussing this with other people:
The reason why California has two regionals is most likely because of population, the size/potential size of player base, distance, and lack of available regionals on the West Coast.
#1: Everyone knows how heavily populated California is these days a gold mine of Pokemon players.
#2: California States have consistently had much higher attendance than any other area of the U.S., and Washington has very high numbers, as well. So naturally it makes a little sense for a regional to be placed in Nevada or North California.
#3: California is worse than Florida when it comes to tourney distances. There are few areas of the country (other than Wyoming, etc...hehe) where you can drive ten straight hours, yet not be anywhere near a regional, and California is one such area.
#4: Like I said, lots of people live near the Pacific; yet it's a geographically giant region, so distance is a pain for players. Meanwhile, most people on the East Coast have no problem at all getting to a regional if they dedicate 5-6 hours of driving. Having a Sierra Nevada Regional balances this out.