The reality is that TWOK could
have been subtitled 'Kirk has a really bad day'.
I mean, it's like the way he ignores basic regulations when Saavik tries to quote them at him, resulting in deaths onboard the Enterprise. Kirk could
just be taking his eye off the ball in a number of the areas you describe.
Absolutely. But what troubles me most about that scenario is that it's one we've seen before, in the previous movie. Decker warns Kirk about not using the warp-drive before it's ready, and Kirk flies the Enterprise
into a wormhole and nearly crashes it into an asteroid, a fate avoided only because Decker realized that an engine imbalance would knock out primary power to the phaser-banks-- something he knew because he commanded the ship for its entire reft and knew every system upgrade. It's only after McCoy yells at Kirk that the latter realizes his obsession with the Enterprise
could get everyone killed.
I'm not saying Jim Kirk is a bad commander. But he's clearly a little out-of-touch with what it means to sit in that chair, and it isn't until his double-bluff with Khan late in the movie that he really starts to get his shit back together in any kind of meaningful way. The whole thing was just meant to be a fun-ride for Kirk's birthday anyway, so chances are he's having to adapt to starship command again on the fly after a decade of being behind a desk, and he just isn't coping very well.
Kirk was out of step, but that doesn't mean he'd have missed an important detail such as Reliant
being assigned to Genesis. His having been absent from the captain's chair for several years shouldn't have prevented him from putting two-and-two together and realizing Reliant
must have gone off the grid for them to be asking Marcus to hand over the Genesis materials. And if Kirk really did
on its mission and forgot about it, he should have been relieved of duty immediately