One of the missed opportunities in TOS, in my opinion, was the lack of moments or circumstances which would have left Dr.McCoy at the helm ordering people around in a moment of intense crisis.
While the Captain and his XO were routinely rendered incapacitated, captured, busy or otherwise unavailable, Scott would usually take command, which was probably for the best as McCoy and Scott were both Lt. Commanders during most if not all of TOS and Scott knew infinitely more about the Enterprises' workings and operation than McCoy (loved all the Scott-in-charge moments btw).
...But that is exactly why such a moment where Bones would have to make the tough decisions and ultimately save the day or at least in part contribute by way of his unorthodox and makeshift commands an interesting angle for the show to explore. I mean from all the times where Bones was passed over and even seemed uninterested in any kind of responsibility I was half-expecting him to cry "Jim, I'm a doctor, not a Starfleet officer!"
Now i'm not suggesting McCoy suddenly turn into a tactical genius or academy strategist but I would have liked to see him bark out a few more orders.
What does everyone else think?
there's a book called "doctor's orders" with this premise. Personally, I think it's a silly idea. Doctors are staff officers, like a chaplain or doctor would be in today's navies. They're not in the command line.
I didn't like it when TNG did it with Crusher and Troi for the same reason. Command isn't just a matter of rank.
It's also pretty silly for a CO to leave the ship on 98% of the away parties and take his XO with him. TOS doesn't exactly steep itself in military realism anyway so why not have one of the main characters who holds rank have to make the tough decisions for the crew.
The president of the United States doesn't have to know how to work an engine room to order a carrier taskforce around the world by the same token.