Why are Californian Super Mutants generally friendlier than the capital wasteland ones?

The short answer: There are two seperate and distinct strains of Super Mutants, those bred on the West Coast at the Mariposa facility (seen in FO 1, 2, and New Vegas), and those from the East Coast, bred at Vault 87 (seen in FO3). They are both the result of experiments with the Forced Evolutionary Virus (FEV), but the use of differing strains produced two distinct Super Mutant populations. The same name being used for both populations is largely the result of the Brotherhood of Steel bringing the term east with them from California.

That said, the FEV's effects vary wildly across different populations - the Mariposa Super Mutants come in a variety of strains (i.e. Nightkin) with varying levels of intelligence, and on the East Coast, we see in Fawkes that not all Vault 87 Super Mutants are completely dumb. Furthermore, the vault 87 mutants show a level of cohesion, organization, and planning that is not reflected in their admittedly limited linguistic capability, so they may not be as dumb as they look.

Finally, I wouldn't call the west coast super mutants 'friendly' per se. While it's true that there are a few that aren't violent and hell bent on the destruction of humanity, they're still the exception rather than the rule.

The wiki article on Super Mutants has more details, and the links to the Vault 87 Super Mutant page in particular is helpful in explaining the distinct origin of the east coast mutants, as well as where in game in Fallout 3 to look to learn more about them and their history.