The film presents a thinly veiled aesop on the dangers of relying too much on technology- which is exactly what modern films have done with the pioneering technology behind the special effects in this film.
Probably unintentional, but the second movie makes for a fantastic warning against the dangers of irresponsible activism.
Even better, in the case of inconsistencies with modern dino knowledge (like the absence of feathers), it is mentioned that Dr. Wu had been mixing and matching DNA, then just waiting to see what grew out of it. If it didn't "seem" right based on current knowledge about dinosaurs, he'd go back to the drawing board, and try a few revisions. If Wu had seen some feathered dinos well before anyone knew about them, then why wouldn't he consider it a "glitch"? There's even a line somewhere in the novel about the JP dinos only being as close to actual dinos as they can guess from modern scholarship by folks like Dr. Grant. It seems Crichton wrote in his own defenses against Science Marches On!
In the first film, Nedry has a photograph of J. Robert Oppenheimer taped to his monitor. This is amusingly appropriate considering that Oppenhemier, who worked on the Manhattan Project, felt similarly about the Atomic Bomb that many of the main characters in this movie felt about playing with dinosaur DNA.
In Tresspasser, John Hammond himself even mentions the parallel significance of the impact their work would have on the world with the Bomb.
Hammond: We were planning to conquer time's power over life, its power to extinguish and erase. It would change all our lives, as profoundly, as irrevocably as the atomic bomb.
The first film pioneered new special effects technology. Soon afterwards, films started relying too much on special effects and not enough on their human aspects. This parallels how John Hammond relied too much on technology to run the park and not enough on human beings.
Every biological inaccuracy shown by the movie and the book can be explained by the fact that the scientists who made the dinosaurs screwed with their genetics and may have even tailored them to fit the expectations of visitors. A nifty way of averting the pitfalls of such a work when Science Marches On.
Jurassic Park's Science Marches On-style of genetics offers some Fridge Horror as well. Considering that the dinosaurs look a bit different and more accurate with each film, Ingen may well have euthanized the animals that were proven to be scientifically inaccurate, only to replace them with improved ones.
The film's "velociraptors" have, let's face it, a LOT wrong with them. The size we can chalk up to being a different species mislabeled, but each film depicts them differently, and distinctly un-feathered, something we now know is quite inaccurate. So... in the third one, they gave the male raptors... mohawks. Of feathers. Ok, sure, they're trying. But maybe these changes in the appearance and physiology are the raptors' DNA overtaking the amphibian DNA used in their creation. Each new generation of raptors is becoming more "real", and in a few decades, Isla Sorna will have fully-feathered, scientifically accurate raptors.
Sam Neill said in a making-of for JPIII, when describing the new raptors, "It's almost as if they've evolved."
Not to mention that explains why the Raptors became less and less psychotic.
A neat idea if not for the fact its practically worthy of being a doctoral thesis in Art Major Biology.
It can be universally agreed on the Nedry is a massive Jerk that brought about his own doom, but take a moment to think of what might have happenend if he had never shut the park down like he did. If the events of the first movie/film had not happened like they did ( with a relatively small start up staff and a handfull of guest) then such events might have happened much further down the road, when Hammond had opened the park to the general public.
Tim's idolization of Dr. Grant goes to very subtle levels—he's even wearing the same outfit (denim button down shirt, bandana around the neck, white khaki pants, and a brown belt), with minor differences (Tim's shirt's unbottoned, different color bandana, and shorts instead of pants).