The Klingons end up killing the entity impersonating God. Which, if you think about it, is what Klingons did to their own gods! "They were more trouble than they were worth."
While Kirk soundly rebukes the "God", it should be noted there's nothing necessarily preventing it from being the inspiration for deities across the universe. Certainly, it can reach out to psychics across the universe and speak to them or it wouldn't have been able to talk to Sybok.
Spock's uncharacteristic faith in Eden shown in the TOS episode "The Way to Eden" is because he secretly believed in what his brother was searching for.
Why would Starfleet send a starship that's literally falling apart, undercrewed, and generally unready for service to solve the Nimbus III crisis? They weren't sending the Enterprise. It was basically just a taxi for sending James Kirk, the guy who talked his way out of omnipotent aliens, tied multiple computers into knots in 15 minutes or less of conversation, and has hosted multiple contentious political conferences and delegations. The cult on Nimbus III is about 30 guys armed with sticks and pellet guns, and Starfleet could take care of them in minutes if they approached it as a military problem. They were sending in a hostage negotiator, and just didn't expect him to cut straight to pretending he was playing Rainbow Six. They also had no idea Klaa would get in on the action, either.
A possible reason for the numerous problems the almost mint-condition Enterprise-A is having in this movie? It was in Spacedock during the Probe's sojourn to Earth.
Alternatively, Roddenberry suggested it's problems were because it was actually the Yorktown, having been renamed and rushed back into service after the loss of the Enterprise, hence why it comes across as a second-hand ship.
If Scotty knows the ship "like the back of his hand", why does he end up smacking his head on an overhanging bulkhead? Because he was likely thinking of the Enterprise, not the Enterprise-A. Furthermore, it's likely that not all Constitution-class vessels were refit in exactly the same way, particularly if this ship was originally the Yorktown.
Or, maybe while Scotty and the crew were away on Vulcan, Starfleet took steps to ensure that something like what happened in Star Trek III: The Search for Spock never happened again by making changes and modifications that he wasn't made aware of. In other words, all future starships will be "Scotty-proof" to prevent sabotage by even the best engineers. So the ship is "falling apart" as Scotty is trying to undo the changes and return the ship to a state he's more comfortable with.
It's never outright stated, but it's a safe bet that Kirk's greatest pain is the death of his son.
Or Edith Keeler.
In what is very likely a combination of both Fridge Brilliance and Fridge Horror, there is a lot more going on during the row, row, row your boat scenes than at first appears. First off, depending on how you look at it, this is either three best friends on vacation shooting the shit over a few beers, or three very lonely work colleagues with few other real friends, no real social life and no family who have no choice but to vacation together. This ties in with the general theme of aging and loss that is running through films 2 through 7 with regards to Kirk and Picard; where you can go on all of these wonderful and exciting adventures, visit incredible planets and meet exotic aliens never before seen by any human, but when the journey is done, you will be coming home to an empty house because the rest of your life has passed you by. Secondly, Bones's anger towards Kirk recklessly endangering his life on the mountain is very likely foreshadowing the revelation of his secret pain later on in the film where he was forced to turn off the life support for someone that he cares deeply about.
Mind you, it's almost certainly just them hanging out because they've spent the better part of 10 years together.
It makes perfect sense Klaa would be snooping around Sol (which is why he shot the Voyager probe). He's trying to get some action and getting into a petty fight with a Federation ship would be just so cool to him. It also explains how he knows there's an emergency - he got the news of Nimbus III from the Federation broadcast, not Klingon.
Sarek never muttered "So human" at Spock's birth. Remember, Sybok is delving into Spock's pain, not memories. Spock's "Well Done, Son!" Guy complex is so ingrained he probably feels like Sarek felt that way every second of his life.
Vulcan infants can remember the moment of their births - is it possible Spock can remember (albeit subconsciously) incidents that happened in utero?
When members of the Enterprise crew sneak into the bar in Paradise City, the Caitian table dancer attacks them. During the struggle, the Caitian is knocked unconscious and thrown into a pool of water. She would probably drown (being unconscious) for doing nothing more than defending her place of employment from nighttime intruders. It's a cruel move by the "good guys", but the movie treats the innocent victim as expendable.
Obviously, for whatever reason, once it's flushed and resealed the waste is vented right into space. Which, when in spacedock, would mean probably splattering some poor maintenance worker's windshield.
The same reason you can't use train toilets in the station. Anywhere else on the Enterprise they probably just use the transporter...