There would need to be a POD millennia back in order to have an Inca-level civilization in California. California's environment is so conducive to a hunter-gathering-fishing lifestyle, which the hundreds of tribes inhabiting the state depended, that by the time of European contact OTL, the transition to agriculture still hadn't happened, just in some cases various kinds of horticulture. And interestingly, even though maize cultivation had spread to the Southwest and the eastern woodlands before 1492, it doesn't appear to have ever reached California, the Great Basin, or the Pacific Northwest.
But, no problem, let's assume that Mesoamerican agriculture had reached California millennia ago. That, combined with the high carrying capacity of California's environment, the Sacramento/San Joaquin river systems, and the abundant coastal resources, could result in a very high population by ATL 1500 - perhaps nearly as dense as Mexico's at that point - and with a few more developments in societal organization, there could be a large imperial state occupying most or all of California.
The next problem though, as with anywhere else in the Americas, is the virgin soil epidemics. There would almost certainly be strong trade links between Mesoamerica and California in this TL, so as soon as the Europeans reach Mexico, their diseases are going to race to Calfornia. In OTL, it only took about 20 years after Cortéz's conquest of the Aztecs for another conquistador, the Portuguese-in-Spanish-service João Rodrigues Cabrilho, to explore the coast of California. So, assuming this gap holds, the Spanish (or other Europeans) who reach California after a 1520's conquest of Mexico will find the Californian empire decimated by disease, just as De Soto found the chiefdoms of the Southeast in utter collapse during his expedition. And since this California will have a lot more in the way of resources and riches than OTL's, the Spanish won't ignore it for the next 250 years as they did in OTL - they'll likely start moving in right away.
So, there's basically two outcomes I see:
If the disease impact is especially severe, California just becomes an extension of Mexico, easily subdued, settled, and mestizo-ized. Perhaps many of the original California cultures survive and eventually recover from the epidemics, but at that point they'll be living as serfs on Spanish haciendas, just like the Nahua, Zapotec, and Maya.
Or, if by some luck the disease impact isn't as severe, then the Spaniards may truly be up against another Inca power, and this time, as others have said upthread, the dice roll may not go in their favor. They may be defeated in battle with this state's army and withdraw to Mexico, and spend the next century either re-attempting a conquest, or settling into a trade relationship with the Californian state; or, they may reach a stalemate or some sort of accommodation, where perhaps southern California comes under Spanish rule, but the center or north is able to maintain its independence. How long an arrangement like that can last, who knows - California is not nearly as inaccessible as the Andes, so the demographic pressure from Spanish Mexico is going to start pressing in on them eventually, even if they escape an initial conquest.
Awesome idea, though, I'd love to see a timeline.