Kruge is sullen after the Enterprise self destructed and most of his men killed. But hes not sad because of the loss of his men or his trophy, hes sad because Kirk massively outwitted him. THIS is why hes positively deranged when fighting Kirk at the end.
At first, it seems unfair Uhura is left behind. But it actually makes perfect sense: if you're hijacking the Federation's flagship and heading to an uninhabited planet, why would you need a communications officer? You'd have no want or need to talk to anybody else.
Also, after beaming to Enterprise, Kirk offers everyone else an out "Dr. McCoy and I have to do this, the rest of you do not." The crew stands by Kirk and goes with him to Genesis. They'd all just broken McCoy out of Starfleet's funny farm, so had to vamoose one way or another, Uhura hadn't done anything (except lock "Mr. Adventure" in the closet). Kirk hadn't planned on taking anyone else with him in the first place.
The novelization also adds that she helped to cover their escape with technological trickery, leading to her taking refuge in the Vulcan embassy with Sarek - legally, she would be considered an accessory regardless by helping them get to the Enterprise, knowing they intended to steal it. Might as well clear the board long enough for the others to get to the bridge and power up the ship without anyone questioning what's going on.
In the previous film, Spock sacrificed himself to save the Enterprise. In this film, Kirk shows he values his friends more even than his ship, and sacrifices the Enterprise to get his friend back. In the end, Kirk couldn't avoid losing something he cared deeply for, because one way or the other he had to suffer a humbling loss to lose the idea that there's no such thing as a no-win scenario.
The first two films had the Enterprise power up its engines and thrust forwards to clear its moorings. This time, the Enterprise instead flies backwards until it exits Spacedock, while the pursuing Excelsior exits Spacedock in the usual forward motion. While this realistically was just based on where each respective ship was parked inside the complex, thematically it represents that unlike the first two films, this flight of the Enterprise was not sanctioned by Starfleet.
Imagine what would have happened if none one realized that Bones had Spock's katra; Spock would die again when the Genesis explodes and Bones would be driven to insanity or worse.
Although we keep calling the boy that they rescued off the Genesis planet Spock, in actual fact he wasn't. He was an individual with completely different experiences, memories, thoughts and feelings to our Spock. We can argue all day as to who the rightful owner of the body is, but the fact remains that when our Spock gets that body back, they murdered the person that was already there without a second thought. And worse, one scene that was thankfully cut from Star Trek 4 has Saavik revealing that she actually became pregnant thanks to her helping him through the Pon Farr - a child that technically isn't our Spock's but the Spock who is now dead. Imagine waking up and discovering that you not only had sex with a work colleague without wanting to, but that you impregnated her. Considering we never see Saavik again (her role being cut from Star Trek 6 in favour of Valeris) it might still be true for all we know.
Some of that particular horror can be offset by the fact that this Spock (for lack of a better name) was, in many ways, a blank slate - the Genesis effect rejuvenated Spock's body, and then accelerated his growth so that, from the moment Saavik and David discover him, appearing about six or so, by the time that the bird of prey flies off and Genesis destroys itself, he's now about the same age as Spock was at his death, so bare minimum, a good forty years of progression, in the span of a few days at most. And, based on the connection that his body had to Genesis, the fact that he was unconscious from the escape to the delivery at Vulcan... It's entirely possible that the "mind" of the body recovered at Genesis died with the planet, leaving the body brain dead.
At some point, someone states that the child's mind is a "blank slate." This Troper took that to mean that Spock's mind was split between the child and his "Katra" in Bones, like a brain's two lobes being separated. It seemed like Spock's higher consciousness was in Bones, while the simplistic natural reactions were in the child's body, and that all the ceremony on Vulcan did was re-merge the two. So the child didn't necessarily "die."
Saavik blames David for his use of protomatter in the Genesis Effect, effectively pinning many of the lives lost over Genesis - from both movies - on him. Unfair, perhaps, but he seems to accept her judgement. Thing is, the bigger problem for Genesis, based on the briefing seen in both this and the prior film, the Genesis device was meant to be used on dead bodies - think the moon as it is today, barren and uninhabitable by life as we know it. Khan detonated the Genesis device in a nebula, forcing the effect to build a planet (possibly even a solar system? The origin of the sun of the Genesis system is unclear) effectively wholesale. The Genesis planet's eventual destruction may have been as much due to the failure of using the device AS INTENDED as the protomatter itself. BUT... Because Genesis failed, and David's use of illegal protomatter became part of public record, the Federation effectively tabled the research into it - and probably prevented a war, because while the Federation would claim moral reasons to never use it (which, organizations like Section 31 would likely have had no hesitation with using it on, say, the Founders' homeworld during the Dominion War, just as an example - out of sight, after all...), they might try to dilute the effect of it by handing over the schematics to other races, with more reason to use it as a weapon ANYWAY. Even if they hadn't, it could have driven the Klingons and the Romulans (and perhaps other powers, like the Cardassians and the Tholians) to join together and strike the Federation first, in fear that the Federation would use Genesis on their worlds. David's use of protomatter, despite the lives lost by way of Kruge in his hunt, as well as the Reliant's discovery of Khan while searching for a suitable test planet, may have actually SAVED MORE lives, by making the project carry the label of a failure. Had he not, the various Alpha Quadrant powers might have erupted into a war that could have torn the Quadrant apart.
Kruge is certainly drawn up to be a mustache twirling villain with questionable motives and tactics, but his accusations that the Genesis device is a horrific doomsday device are 100% legit, and the Klingons, Romulans, etc, absolutely have a right to raise bloody hell. Considering that surely the planet destroying feature of Genesis could be accomplished without a new planet being created, ESPECIALLY considering the latter part failed, really makes it look like a ruse for a planet destroying weapon. Which in the meta sense it was in the early concept, the Feds created an ultimate weapon and it was changed because that didnt fit the Gene vision of Trek humans. Also, its worth noting that the late Bibi Besch (Marcus) next played in The Day After, and she said her attitude toward the device would have been far less optimistic had she played in The Day After first.