i suppose in the most literal sense, he’s a good leader because he inspires his subordinates to follow. no matter how ill-advised or hairbrained a plan seems, his crew will always follow through. granted those same ill-advised, hairbrained plans are a reason why many would argue he’s a bad leader, but the Romulan episode goes to great lengths to show how he never makes those kinds of decisions lightly, despite making them often. the alternate version of that same episode in SNW shows that a more measured, Starfleet response there just wouldn’t have worked, so there’s also an element of Doylist logic there- he’s a good leader because the writers say so, and his actions aren’t the best course of actions for their own sake as much as they are because they’re his actions.

the movies definitely make him more fallible, and if Kurtzman-era Trek has one single theme, it’s the deconstruction and destruction of the infallible hero-captain archetype. but even then, Kirk being both The Greatest Captain and a space cowboy are load-bearing pillars of the Trek mythos at this point

TL;DR kirk’s intuition has plot armor and you can’t retcon that without basically retconning all of Trek because of his in-universe and real-life mythic status. he’s an exceptional captain, and the exception that proves the rule