Except that nobody, to my knowledge, has ever identified "unrealistic command structure" as a serious flaw in Star Trek to date. There's nothing to fix.
Then why the reboot?
The lack of realism is deliberate, maintained for dramatic purposes. Starfleet protocol serves the characters as needed, not the other way around. Realism is suffered until it runs into something more important.
Not only is that stupid, that's the kind of thing that makes a lot of movies stupid.
Was it Starfleet's decision when Picard decided to take over an entire fleet in "First Contact?"
Captain Picard, an experienced senior officer who had previously commanded fleets before, and was uniquely qualified to fight the Borg.
In fact, Kirk in this situation is more or less an ACTING Captain. This is how Memory Alpha defines an Acting Captain:
The position of acting captain is bestowed upon an officer or another officer aboard a starship when the ship's regular commanding officer is unable to command for an extended period of time.
And that position would be meant for a qualified officer.
Memory Alpha goes on to cite examples like Data becoming an acting Captain in the TNG Episode "Night Terrors," and then again in "Gambit Part 1 & 2. Harry Kim took over as acting captain for Voyager during the episode "Course: Oblivion" when all the senior officers "dissolved."
And both were commissioned officers within the chain of command.
So considering Pike left Kirk as Spock's First Officer, and Spock is off and away somewhere, Kirk feasibly can take over since he is next in line, and the commanding officer is incapacitated.
Kirk is not a commissioned officer and therefore is unable to be placed within the ship's chain of command. He has no experience and would be a danger to the ship, it's crew, and whatever mission they hoped to accomplish.
Ok, my 2 cents on the Kirk taking command thing. From what I recall of spoilers from way back, Kirk is denied officer status after cheating on the KOM test. It's entirely possible that Kirk is a Lt. much like Saavik was, but is getting punished by a grouchy old Admiral.
The fact Saavik was wearing LT rank has been nitpicked plenty of times, and so far the only explanation that makes sense is that she was a cadet officer, not a commissioned officer. And if Kirk was commissioned, he would be an ensign, and be the most inexperienced person on that ship.
If Pike gives him his rank back, which is probably within his rights during a combat situation, then Kirk is actually in the chain of command.
And there would still be plenty of more experienced officers on board more qualified to take command in the event Pike and Spock are unable to.
Since he's Kirk the wunder kid and did really well at SFA, and gets his Lt. rank back, he actually would be 3rd in command if Pike ordered it.
The way I read it he was Kirk the problem child with problems with authority and was being punished and was almost kicked out of the academy, not an officer who was being punished.
Pike and Spock are gone. Sulu and Uhura would then be the same rank as him, but probably didn't take the same advanced command courses Kirk did.
All officers receive command training, or they wouldn't be officers. The function of an officer is to command.
McCoy isn't in the chain of command, as per canon. Remember, fricking Leslie got command over McCoy in TOS. Geordi gets command over Troi or Crusher.
But if it was just them and a cadet, they would still be the ones left to take command. Remember, both Troi and Crusher were left in command of the ship when there was basically no one else left to do so.
I'm getting the impression that it doesn't really matter if there's any kind of realism involved, because the people excited to see this movie are blind to anything that might be negative about it.
Captain X - I think you're not taking into account that the only reason Kirk isn't a comissioned officer like the others is because of the Kobayashi Maru incident.
We don't know that for sure, all we know for sure is that he was being punished and was being considered for expulsion at the time of this emergency, and that despite obvious manpower shortages, he was still singled out to have been left behind. Not exactly what happens to a capable cadet.
For all we know he could otherwise have been top of his class. Under those circumstances, Pike giving him the XO's position in am emergency doesn't seem so far-fetched.
Yeah it does, because he's a cadet, which means his training is not complete and that he is not a commissioned officer. This also means he has no previous experience, making him the least qualified person on board that ship, so not someone you'd want to make an acting XO or any position within the chain of command.