I've always just assumed that Spock was uncomfortable in command situations and tended to overcompensate by taking refuge in his Vulcan training and becoming "Supervulcan". Even in TWOK he indicates that as a teacher (like his Mother) on a training mission he's comfortable in command, but an actual mission is quite another thing altogether.
Yeah, but that was Spock speaking after becoming, as he viewed it, a teacher, and further indicating that in an "actual duty" situation, the senior officer on board must assume command. Plus, he was making an argument designed to ease Kirk's potential conflicted feelings about taking command. Several years later, he has absolutely no problem taking command, and quite skillfully, in TUC.
In some episodes of TOS, Spock is a talented commander who makes reasoned decisions and earns the respect of his subordinates. "Who Mourns for Adonais" is perhaps the best example of this, but there are several others ("The Mark of Gideon" comes to mind). But in other episodes, he's closed off ("The Paradise Syndrome") or downright strange (as in "That Which Survives").
So it's quite inconsistent. The producers did a far better job consistently portraying Scotty as an apt starship commander than they did Spock.



But I've never really been able to come up with a good behind-the-scenes rationale for it. Maybe it was Shatner exercising greater creative control over his character than Nimoy did. But that is an unsatisfactory explanation, because some of the crazy swings in Spock's characterization (though not all) occur within S3, when Nimoy (and everyone else) already knew darn well that Spock was the "breakout character." One thing that jumps to mind - Spock is wildly different in "The Mark of Gideon" and "The Paradise Syndrome" than he is in "That Which Survives" - and he was in command of the ship for substantially all three of those episodes.