I am glad this subject was brought up, because when I was going through TOS a few months ago, I was rather shocked by how Spock was treated at times by his subordinates. I can't point to any specific examples that haven't been noted, but I certainly got the impression that the writers never agreed on Spock's role, or the relationship between Vulcan and the Federation.
Take, for example, that McCoy said early on the Vulcan was conquered, implying that the Vulcans didn't enter the Federation voluntarily (though this is debatable). I recall it being mentioned later in the series as well.
Spock's race was sometimes Vulcan, sometimes Vulcanian. It wasn't simply a matter of them not settling on a name until later in the show, as Vulcanian was used in the third season as well.
About as progressive as the 60's gets. Spock gets a lot of insubordination from junior officers in TOS. No way the XO should have been getting that much mess from the crew.