What Leonard Nimoy brought into Star Trek was his interpretation of Spock, as someone who will always be different, an alien, a misfit, but at the same time respected, a part of the gang, a good friend. From interviews and histories, the picture emerges of Nimoy having a pretty large say in Spock's characterisation and backstory.
As for cultural differences, the classic Trek Line was always "oh, we used to discriminate based on religion, but we got over that." It was a little heavy-handed, thus the recognition in The Next Generation that religion was still around, but it was treated as something that enriched a character's background and was not allowed to be an excuse for intolerance. Intolerance within the Federation didn't play a major role until Enterprise, and by that time I had lost interest in the franchise (the Terran supremacists also seem cribbed from Babylon 5).