And the West Coast super mutants somehow didn't go through the same process and so they aren't quite as aggressive?
West Coast super mutants are dipped into FEV, the ones on the east are gassed. And Vault 87/Institute FEV is different from the ones used on the west coast, and creates an entirely different kind of super mutants. Its not surprising the effects of the transformation are different as well, due to differences in strain and delivery method.
Also, you have peaceful SMs in F4 too,
Literally one, who is pointed out to be rather unique among his kind.
Super Mutants are always hostile because in Bethesda's eyes they are the orcs of Fallout. Another target practice for the player to put bullets into. It shows the laziness of their writers that they didn't bother coming up with interesting characters that aren't human or Ghouls.
Actually, its more likely they do it to keep them relevant.
West Coast Super Mutants lost any sort of unique narrative purpose after Fallout 1, because they are one trick ponies. It's why both Fallout 2 and NV have done nothing to progress the west coast super mutant story besides retelling the same "WE JUST WANNA GET ALONG, BUT RACIST HUMANS KEEP BOTHERING US WAAHHH!!!!" story again and again. Nothing actually develops in this story, the humans don't become any more or less racist, nor do the super mutants become any more or less accepted, despite the passing of a literal century. Its this completely static narrative quagmire due to Obsidian's staunch refusal to actually
change anything. It's a fate befallen the WcBoS as well, which is why both Fo2 and NV used the same "we are isolationist to the point that we can't stand up to anyone or anything anymore, so we just sit in our bunkers all day watching the world go by!" plots for the BoS. You could entirely remove Jacobstown from New Vegas and nothing would change, because super mutants are that tangential to the plot, because nothing was done to develop them or integrate them into the overall world past what they were in Fallout 1.
That's not good writing, nor does it create any interesting characters, that's just going Ctrl + C, and then Ctrl + V, between games.
Vault 87/Institute super mutants manage to be a large part of the world, and the game's overall narrative, in both Fallout 3 and 4, despite being overly hostile outside of 1-2 unique individuals. And seeing conflicts between various species fighting for dominance is more interesting then seeing a small town of about 15 super mutants who do nothing all day, ala New Vegas. And the uniqueness of the rare non-hostile Super Mutants, like Fakwes and Strong, makes them stand out more in the long run then every super mutant acting basically the same.