It's more of a popularity contest if anything. I think in reality, Malcolm would be ideal for 3rd in command. If both your captain and 2nd in command are killed/incapacitated then you're probably in pretty bad situation and need someone with combat experience to get you out of it. The Tactical officer would be more ideal in this situation.
I always felt the same with TOS. And sorry to place the race card, but I think Scotty was only chosen because they didn't want an asian man, a black woman or a Russian to command the ship while the captain and second were on a mission.