I'll start by giving a few examples of what I mean... You can either try to give an answer or add new items to that list... Your choice.
I'll be the dull sort...
1) How were the Ba'ku able to expulse their unruly offspring from the planet after having renounced technology and only using medieval tools for about two centuries and while we're at it.
They probably still kept their starships parked in a cave somewhere. And the rift in the first place no doubt was along the lines of whether to use those starships or not...
The Ba'ku are portrayed as somewhat pacifist in their chosen mode of existence. But deep down, they are likely to be afraid instead. They are huddling inside the Briar Patch, having fled from a star empire of some sort. They didn't exactly flee oppression and violence; like so many colonizing parties in Star Trek, they denounced the technology-dependent way of life back home. But they still hid. Letting the youngsters take the starships for a ride around the neighborhood might get everybody killed, or at least dragged back home.
Except it didn't, because when the Son'a left, the Briar Patch was already besieged by another star empire, the UFP. Whether the Son'a returned to their ancestral home, or just set up shop somewhere else, is left unclear in the movie, but e.g. Memory Alpha quotes the latter model, based largely on cut scenes and illegible computer readouts.
How were these offspring able to acquire technology with Luddite parents who wouldn't teach them anything about it?
The folks of which the Ba'ku and Son'a were part probably were technologically highly advanced overall. The Son'a knew how to collect the fountain-of-youth particles when the best minds of the Federation could not. The Ba'ku had Data figured out in no time flat when the best minds of the Federation had to wait until "Datalore" to even discover that Data was a positronic machine created by Noonien Soong.
Also interestingly, the Son'a were manufacturing Ketracel White for the Dominion back in the war; although it was never stated the UFP could not do the same, we might jump to conclusions here and speculate the Ba'ku originally came all the way from Gamma Quadrant, with all the related requirements on capabilities.
Simply giving up on the luddite credo might allow these people to become tech wizards (again) overnight. It's not as if the Son'a would have been specified as bred in the Briar Patch - they would be "youngsters" rather than "children", already educated in the tech ways when their parents chose to flee.
2) If Guinan had such a hard time forgetting the Nexus and described it as being "wrapped in joy", how come both Picard and Kirk got sick of it in a matter of minutes?
I'd speculate the Nexus is simply a shuttle flight arranged by a fairly advanced culture: it does what the passengers want it to do, including providing superb inflight entertainment. Its regular route takes it close to planets so that the passengers can opt to leave or board. And it certainly won't stop passengers from leaving if they so wish. But Guinan's ghost would have had no desire to leave, whereas Kirk and Picard were on a mission.
How come that Picard's most urgent wish was to be surrounded with children since he disliked them so much that he told Riker that one of his most important tasks was to keep them away from him?
What's that annoying quote? "The lady doth protest too much". Picard always wanted to have kids, which is why it was so painful for him to be surrounded by the kids of others when he had none...
3) How come the Klingon BoP is able to site to site transport four hundred tons of water and two whales but not people?
The heroes repaired it. That was quite a major plot point in the movie...
1. Why do the Kazon just sit around all day outside the Ocampan city in the desert like idiots if they are a space faring people that could simply go in search of greener pastures?
Because they want to pillage the Ocampan city. And if they give up, some other Kazon sect will take their "pole position" and get to the riches first.
Which is also why these Kazon are short on water. There's plenty around, but this bunch cannot leave because leaving would mean losing.
The Kazon can no doubt tell that this is the crucial hour - the Caretaker starting to die has all sorts of observable consequences that Neelix points out and the Kazon no doubt could spot as well. This is definitely not the time to take a break!
2. Why in the world would Shinzon want to destroy all life on Earth?
No bloody idea.
But he was pretty pissed off at having been manufactured for a purpose. If him existing was a problem, confounded by him soon ceasing to exist, then inflicting nonexistence on others would seem prudent. He had already handled some of the Romulans, and might well return to finish that side of the business. Doing the humans was simply within his means.
3. Why would you even make it an option to disable safety protocols on a Holodeck?
For the thrills. Many hobbies are based on the thrill of danger to life and limb, and outlawing suicide is no longer fashionable today. And judging by "Ethics" and the like, it supposedly isn't in the 24th century, either.
It is noteworthy, though, that the safeties in the adventures are turned off by people with top authority: LaForge and Torres, chiefly. Or Chiefly.
4. Why does Red Squadron turn its leaders into relentlessly disobedient and lying douchebags that seem to consistently get people under their command killed?
Oh, Red Squad only ever appears once, in DS9. The first bunch to do that was called the Nova Squad, in TNG.
I guess it's a way of standing out. Leaders lead, but not all leaders manage to inflict mayhem during their study years yet.
Timo Saloniemi