Why is he controversial? The California Indians were NOT living in an Edenic paradise before he arrived. They fought each other in tribal wars, they had high infant mortality (as did all hunter-gatherer groups); and their lives were much improved when they learned farming and were associated into non-warring communities by the Spanish.
Of course, they didn’t get a Jeffersonian republic; but some of their much-vaunted “customs” weren’t better than what the Spanish had, and weren’t worth preserving.
(the above represents a non_PC viewpoint, and also assumes that Christianity is better than animism and shamanism)
For the well-educated there is NO controversy.
According to some nativist American-marxists, Junipero Serra wouldn’t let the people (whom he taught farming and civilization) to speak their own language but had to learn Spanish, which they did ... only 400 years ago, but “ ... never let a good crisis go to waste ... “
California's missions were also military outposts, they were also industrial/agricultural centers in need of labor and designed to export the riches believed to be abundant in the new world.
"Weren't better than what the Spanish had" suggests that you know that infant mortality etc. were no better in Madrid or London than on the Monterrey Peninsula of today's California...and I sincerely doubt that tribal wars here were even a fraction as horrendous as contemporary national and religious wars of Europe.
I guess this is a good time to ask you about your opinion of Mexican illegal immigration into the USA and muslim infiltration into Christian Europe and America today; both organized assaults on the existing culture which some say is "no better than...".