Hamilton plugs into Mercedes with just one click. He's a plug n' play driver.
He's one of those drivers that does that with a team. Hamilton is all that Mercedes needs. They'd almost just field one car if the rules permitted it.
It's not team-driver intrigue or anything conscious by the team against Bottas. And of course, Bottas has his deficiencies, his talent is temperamental.
But I think if one driver fits hand-in-glove with a team - unless the other guy is a real sparkling Fangio whizzkid type - the other guy is inevitably going to get somewhat sidelined from the team. Bottas is unlikely to be driving a car finely honed to his tastes.