Throughout the original movies, the only time Kirk is GIVEN command of the Enterprise is the end of The Voyage Home. Every other time he takes the bridge, he does so either in the face of a massive emergency (acting on his own authority) or, in TUC, because the Chancellor of the High Council asked for him by name. Strictly speaking, the only time Kirk is SUPPOSED to be in command of the Enterprise is in STV, when the ship is falling apart and half its systems aren't working.
Let's analyze this, shall we? In TMP, Kirk is given back command of the Enterprise. Even though McCoy stated that Kirk "rammed it down their throats," Kirk also implied to Scotty that it wasn't an easy thing to persuade Nogura. But persuade him he did, and at the end of the film it's implied that Kirk is now permanently in command (and the ST Encyclopedia also conjectures that he proceeds on another 5 year mission as captain.
First of all, even the novelization -- written by Gene Rodenberry, no less -- goes into exhaustive detail of exactly how Kirk ended up making Admiral in the first place. His argument with Nogura happens in that context:
At first Nogura had seemed indifferent and impatient-but Kirk had seen that the Commanding Admiral was also troubled and tired. Logs aside, was today's Kirk a better Captain than the alert and upcoming young Decker? How much had Kirk been damaged by almost three years on the ground in an unfamiliar and unhappy environment? Ordinarily, Kirk would never have risked this direct a confrontation with the Commanding Admiral. But this was the first real challenge Kirk had faced in these past three years and Nogura, however dynamic and fearsome his personality, was also the man who had manipulated him, used him. This was a battle that Kirk was determined to win.
In the end, Nogura caved because Kirk promised him that he was motivated PURELY by the need to intercept V'ger and by nothing else, and then added a the shameless guilt-trip of "I've never lied to you, and I'm sure you've never lied to me." The other half of this issue is that Kirk played on Decker's reputation for being overly cautious at times, which put him in a position to pull rank and take over for the emergency.
As for taking back the Enterprise for a five-year mission, there's NOTHING AT ALL that suggests he remained on board any longer than the actual shakedown cruise. The novelization goes on to suggest that with Kirk's spectacular success in the V'ger incident, he basically had Nogura by the balls and could request just about anything and have it granted. Even if Kirk got what he wanted -- which is far from certain -- that would create a huge amount of tension in an already strained relationship between Kirk and the Admiralty.
In TWOK, Spock is in command but allows Kirk to take the center seat during the mission.
Spock doesn't "allow" it at all, he INSISTS. Partly because he knows the regulations, but mostly because he is Kirk's friend and knows it'll be good for him.
When Kirk returns the Enterprise in TSFS, Starfleet doesn't berate him for being in command, they just say that the Enterprise is to be decommissioned.
And they use every excuse in the books to avoid giving him a NEW command.
Which, as we find out at the end of TVH, they could have easily done; apparently they had a ship already waiting for a crew (whatever it was that wound up being christened Enterprise-A) but they didn't want to give it to Kirk. This makes it another repeat of TMP: the Admiralty wants Kirk off the bridge, and this time Kirk doesn't have a legitimate excuse to push back.
And yes, they DID scatter his crew. In Wrath of Khan most of his original bridge officers are teaching at the academy, Chekov is first officer on Reliant and Sulu is on temporary loan from another assignment (probably Excelsior) for three weeks. NONE of them are supposed to be on the Enterprise in Search for Spock, and given their histories Starfleet is probably very anxious to find other work for them the moment they get off the ship (Scotty got reassigned and promoted before he even left the ship).
And please show me the evidence that these people got their promotions and transfers not because they deserved them, but because Starfleet had some ulterior motive to separate them.
Consider that for a moment: Chekov is promoted to first officer on USS Reliant at a time when McCoy is lamenting "Why don't we put an experienced crew back on the ship?" This begs the question of why Enterprise IS short of experienced officers, why isn't Chekov acting as first officer of the Enterprise? More importantly, why is Sulu taking "any chance to go aboard the Enterprise" instead of being, you know, CAPTAIN of the Enterprise?
The simple answer is that the Enterprise crew didn't just get promoted, they got LATERALLY promoted away from Kirk's command. Only the Admiralty specifically knows why, but at least in TMP it's strongly suggested that Starfleet put Kirk behind the desk for the organization's needs to the complete detriment of his career.
All of the examples you provide are reasons why Starfleet would want an experienced captain and crew out there
Actually, that was the specific reason why they initially wanted him behind a desk, where his experience could do more good for the organization as a whole. The U.S. Navy does the same thing in the submarine service: attack boat skippers rarely get more than one command assignment and NEVER get more than two. I'm told that this is also becoming the case with aviators now, where a two-year combat tour (or two if you're lucky) is typically followed by ten to fifteen years in training squadrons, quietly waiting for retirement.
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