I think Kirk's mistake of not raising the shields makes perfect sense pertaining to him (Kirk was arrogant and overconfident, which came back to haunt him a couple times in the movie), so I tend to think of it as a character-based fault rather than writer's convenience.
How many times has lowering shields, or not raising them, or otherwise not taking what could be perceived as aggressive action
been the right move by Kirk?
In "The Ultimate Computer," Kirk gambles and lowers his shields and Commodore Wesley breaks off his attack. By the book, Wesley should have taken advantage of the one moment he had to stop the Enterprise, but his humanity (which Kirk was gambling on) causes him to pause and call of the attack.
In TMP Kirk does not return scans or go to battle stations (screens and shields) to avoid giving the impression of an offensive posture, contrary to his procedurally minded XO (after the Klingons provoked V'Ger directly and after Epsilon 9 reports that their scans might be being received as hostile shortly before they get de-resed).
In The Corbomite Maneuver, Kirk does not beat a hasty retreat or attempt to harm his aggressive captor when his ship appears to fail, but rather puts himself at risk by attempting to help Balok.
In TWoK it is a mistake in terms of the "by the book" proceduralism with which Lt. Saavik is so fixated and it was a mistake congtingently; it just so happened that in this case a sister Starship was an actual threat. Khan, however, was right in reasoning that a Starship Captain would not see a sister ship as a threat. They really were "one big happy fleet." Khan wasn't counting on Kirk's arrogance
per se, but rather the general presumption any Starfleet captain would be operating under. And it's not like he needed to keep the ruse up forever, just enough time to sucker punch Enterprise with a full broadside. Khan gambled on Kirk's humanity, the assumption of goodwill, in much the same way that Kirk gambled on Wesley's.
Kirk not raising the shields is not Kirk making a rookie move or getting senile, but rather is a moment designed to show Kirk's uncertainty, to show the flip side of all those risks he's taken over the years (as McCoy asks in the same film "Can all your guesses be right?"). The point is to get him to second-guess himself and get him to confront, in his advancing years, his mortality.
The point is not that Kirk is some bumbling idiot, but rather that he is mortal, and that his weaknesses as a character are related to his strengths. In the Song of Roland, for example, the greatest of all of Charlemagne's knights refuses to blow a horn to call for help. He does this, in part, out of pride, but also because his job as the rear guard is to make sure that the King and the rest of his company make a clean exit from Spain. Valiant Roland waits a little too long to blow the horn (he was betrayed by another of his peers and gets ambushed) and the rear guard gets obliterated. Yes, Roland should have blown the horn, but we have to remember that Roland's strength lies in his willingness to do his duty facing bad odds.
Kirk is in a risky business and his success stems from his brilliance as a risk-taker. Kirk makes unconventional chess moves (literally and figuratively) and is not afraid to bluff a weak poker hand. With Kirk as our captain, as a Uhura notes in TMP, "our chances of coming back from this mission in one piece may have just doubled." Kirk is THE MAN, but he is also, just a man.
I think a lot of people watch TWoK and misperceive Kirk as repeating the dumb moves he initially makes in TMP (warping into wormholes and getting lost in the ship's corridor's). If you do so, it is easy to see this moment in TWoK as a mere character fault. Arrogant Kirk flaunting procedure, etc. This is, however, not what TWoK is trying to tell us. It is not that Kirk is a fool, but rather that Kirk finally has to confront failure, aging, and death. He has to, for the first time, really confront the flip side of all those guesses. It's not that our hero is not our hero, but that he has finally been forced to inspect his own clay feet, and it's terrifying.