Spock always said he never wanted command, never wanted to be captain, etc. I think he knew he was not really cut out for that type of position. Also too, there was at times in other episodes, an underlying understanding that Spock was discriminated against because he was half Vulcan and I thought that was partly why the Galileo crew was not respectful of him. And that the episode was exploring what it took to command~ not just superior knowledge and ability to make decisions, but an ability to read and understand people- not just human - because Spock mis read not just his crew, but the species that lived on the planet and attacked them.
And as for Scotty, I thought he always worked well with Spock because he never judged him and always seemed very practical (until you insulted his "bairns")
McCoy is just scrappy and doesn't care what he says to anyone - it is his one fearlessness. If you don't like what he says, tough beans. I like when he says what everyone else is thinking but won't say. Don't we all know someone like that and smile inside when they do it?