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The only legitimate reason to not bring them back would be concerns over how their presence might be akin to an invasive species, or the disease's they may be prone to carry, but even that is a stretch. We absolutely could safely contain dinosaurs if we wanted to, and we also have ample weapons to kill them if they were to escape.

I'd say it has two main themes:

1) "Don't meddle with things you don't understand", such as genetic engineering dangerous creatures on an untested mass scale.

2) "DINOSAURS ARE WAY COOL!!!!!!". That was the movie's selling point.

You're crazy if you think bringing Dinosaurs back to life is a good idea. Imagine dying from getting stepped on by a brachiasaurus or getting slashed open by a rapter. Or eaten by Tyranosaurous. The way people live today, Dinosaurs would destroy buildings and cars. It's a stupid idea to bring dinosaurs back and anyone who doesn't think so should be put in a mental institution.

Major themes of nature v scientific manipulation, greed, reckless power/dangers of modern tech, family, dinosaurs are magnificent and the life finds a way argument was only a prelude to chaos theory imo. But mostly, the film doesn't try to be extremely scientific or smart. It explains the premise in a tight and neat way so the viewers don't need to overthink it; nor should they as it's a film about dinosaurs. There are many flaws, but it doesn't try to expand on the science because that's not the focus of the film; the focus is dinosaurs because people love dinosaurs. If the film was Flock of Condors Park, but went into depth on the serious arguments about the morality of scientific genetic manipulation, most people wouldn't care.

They wanted to make a movie about dinosaurs and Crighton's book, which was a unique idea, was ripe for the picking.

Also, zoos don't have animals as large as dinosaurs in them and elephants aren't predators so I don't agree with that argument. The simple reason to not recreate megafauna is because we probably can't provide a suitable environment for them or it would be extremely difficult. Plus we would somehow have to find all these mosquitos in amber.

Par for the course with Spielberg. Style always takes precedence over substance. Spielberg is a thoroughly commercial filmmaker at heart. You'd be wasting your time to go searching for really concrete themes. Even if you find them, it's not like the movie is really preoccupied with exploring them in a meaningful way. They're just there as storytelling adornments

I'd say the only real theme you can discern would be about man's hubris. It's a (very weak) allegory about man biting off more than he can chew. That's pretty much it

To me the biggest plot hole is simply the notion that if a bunch of dinosaurs were let loose that it would result in carnage and destruction. Dinosaurs aren't monsters, they're just prehistoric animals. Doubtful that their behavior was all that different from modern animals

If a zoo's animals were to be let loose, including all of their apex predators, I highly doubt the animals would go on a killing rampage. Even predators tend to be weary and avoidant of most other animals unless they are specifically on the hunt. It would go against any animal's instincts to simply destroy everything in its path. Natural selection would select against such aggression because if you're constantly picking fights then its likely that you will quickly pick a fight that you can't win

Of course, none of that matters. The movie is not concerned with accurately portraying scientific ideas, or with accurately portraying the real world in general. It's just, as Scorsese would say, "a theme park"

You know it's based on a book, right?

It's just a movie.

Don’t mess with evolution or nature. Ecosystems are very delicate. When you bring in too many species (invasive species) into a system the system is not going to be able to sustain itself the way you want it to. Some populations are going to be wiped out because if you introduce a predator then then other native species will become the prey and their population numbers will decrease (like humans). Ecosystems are fragile, don’t mess with them or it upsets the balance.