TMP has a HUGE plot hole. A near-god-like living machine, which can digitize entire worlds and star systems and created a near-perfect android duplicate of Illia, never thought to wipe the muck off it's name plate?
That's not a plot hole. There was no necessity in removing that from a nameplate. V'Ger was a living machine, not a curator at the Smithsonian.
Wrath of Khan's entire "two dimensional thinking" thing made zero sense, especially if Khan is the genius he's repeatedly said to be.
You really missed the obvious meaning. Being a self-professed "genius" does not mean one is able to understand the abstract, such as experienced-based, creative thinking, which allowed Kirk to use, then move past conventional Starfleet tactics Khan could not understand. Moreover, his "genius" arrogance robbed him of even considering that his lab-created intellect could be out manuvered by a "plain" human.
And why didn't Khan just beam Kirk up for torture and execution when he took the entirely magical Genesis device?
Khan is an emotional human. As he pointedly observed, he hurt Kirk at that point (killing Regula staff, stealing Genesis & and inadvertently causing Terrell's suicide), and would go on hurting him by leaving him "in the center of a dead world." That was his point. However, he was sensible enough to see if the resourceful Kirk would escape, and if so, be prepared to destroy him with Reliant.
Regarding your "magical" comment,
Star Trek is not
NOVA, or an issue of
Popular Science. It is set in the late 23rd century, and most of what had been created up to that point deals with projections based on real world theories, mixed with fantastic ideas of what could be--or what will never be. That is the history of most filmed science fiction.
If you really have a problem with a so-called "magical" element in ST, then you should have walked out of the horrid NuTrek movies, as they are no more scientifically accurate than the TOS movies.
Search For Spock is pure Vulcan hocus pocus, with not an ounce of realism or science fiction.
The extremes of some ST fans' atheism aside,
Star Trek--to make this point again--deals with concepts that are more than the one-sided desire for alleged "hard science." If it tried, then many things created and maintained from TOS and through the rest of the proper franchise would not exist, such as the mind meld, Q's species, the character in my avatar, and dozens of other powers, traits or events that are not understood or generated by a scientific explanation.
Spock's ageing just happening to sync up with them arriving and leaving... uh huh. Also, Excelsior spluttering to a halt totally ignoring the laws of physics.
You probably buy the never-going-to-happen transporter technology, or convenient time travel, or the entire concept behind the Borg. If so, then you are accepting things that have as much chance of happening--based on current physics--as a gamma radiation overdose transforming a person into a giant, pea-colored superhuman who can hurl tanks across the state, or take mile-long jumps.
Bored now. But there are more. Lots more. And people like to pretend JJ Abrams' Treks invented plot holes. LOL!
Abrams did not invent plot holes, but many see him as the
'roided up practitioner of it.