Paleontologist here.
The appearance and behavior of dinosaurs is largely a factor of speculation. There are a few things that would be updated. The Velociraptors would have some sort of feathery integument, as would the baby T. rex. Maybe some of the animals would show more color than gray, brown or moss-green. But that doesn't take much thinking, and the science of paleontology hasn't been able to ascertain much about dinosaur color, unless preserved feathers are found (they have been and colors include black, white, and sort of an umbery, rusty color- I believe someone else mentions this in a post.)
Jurassic Park is now 20 years out of date. If you're looking to update the science and still retain a compelling story, you're going to end up with something like this:
The crucial part of Crichton's idea was that the amber which preserved the mosquito served as a preservative barrier- a seal which locked away the precious dinosaur blood from contaminants and harm- a simple idea which ultimately proved very compelling for a story.
Now there are definitely issues with this. You're not going to set up a lab and get extinct animal blood from a dead bug anytime soon. Plus, after sitting in a chunk of resin for millions of years there is certainly going to be some mingling between the mosquito DNA and the DNA of whatever it fed on and anything else trapped in the sap. Wouldn't it be nice to see THAT come out of an egg? Yeesh! I degress.
The one thing that people have heard about Jurassic Park if they've heard anything in the last 20 years, is that "you cannot clone dinosaurs from blood in mosquitoes trapped in amber." So how do we move away from that, bsoftut still make dinosaurs? Because no one is going to be amazed by the trapped mosquito/dino DNA idea anymore. They know it. It's part of popular culture, like "don't cross the streams" or "He's been dead the whole movie!" How do we make the core part of Jurassic Park new?
Easy.
One of the biggest developments in paleontological research in the last few decades has been the discovery of soft tissues preserved in fossil bone interiors. These bones come from the badlands, like any other dinosaur fossil, but they are excavated using sterile field techniques and without polymer consolidants (glues) to keep contaminants from entering the bone' interiors (I know this because I have done it). The fossils are then taken back to a sterile lab where the mineral components are dissolved in baths. If the dinosaur bones were truly permineralized (eg- all 'rock') then the entire fossil would basically dissolve in solution. BUT! That didn't happen when the first lab tests of this kind were conducted back in the early 2000's. There was stuff left over after the mineral components had dissolved away. Spongy, squishy, stretchy, soft stuff. Paleontologists have documented what appear to be bits of collagen (connective tissues), and remnants of blood and bone cells from those samples. There are also bits of proteins that may be preserved. This was absolutely unheard of when Crichton wrote Jurassic Park 30 years ago. Now, in the real world accessing DNA hundred million year old soft tissue is not yet viable, but in 1990, neither was sucking out a fossilized mosquito's guts. But it was brilliant science fiction. And while no one has ever actually pulled blood from a fossilized mosquito...
I'm sorry but take a moment and get ready for this realization:
WE HAVE ACTUAL HONEST-TO-GOODNESS DINOSAUR TISSUE AND CELLS. HOLY SHIT!!
What does this mean? It means that there's no more need for the old amber-bug-blood plot line! Now, instead of mining for amber in the jungle playing roulette with mosquitoes (there's no way of knowing what kind of animal a mosquito had bitten just by looking at the thing--Hammond would have had to sort through thousands of mosquitoes before finding one that had actually bitten a dinosaur), you can go to the badlands and look for soft tissue from ANY DINOSAUR YOU WANT. How's THAT for an overhaul? It completely updates the heart of Jurassic Park's story and allows it to remain a sort of beacon for trendy Sci Fi (yes, and you can have your cloning morality play too). It also removes a lot of inconsistencies, like "How did they clone extinct plants? Mosquitoes don't drink plant blood" and for scientists, it seems more plausible because if you want a park with, say, a Triceratops in it, all you have to do is go to Montana, South Dakota or Wyoming, poke around until you find some Triceratops bones poking out from a nice, thick sandstone unit, and BAM- pretty damned good chance you could get some soft tissues out of there.
The second big change for Jurassic Park would have to be the DNA gap-filling. No more amphibian DNA. Birds. They would need to use a more ancient bird, like an Emu, Cassowary, Rhea or Ostrich. These large, flightless birds (collectively known as Ratites) are some of the most primitive-looking birds living. There has been a lot of genetic work done on chickens lately, and chicken DNA might work as well because we know so much about it. In a Sci Fi story it would not be much of a stretch to say that we have control over the chicken genome, and thus could reduce it back to a sort of "stem" state, where the genetic instructions basically say to build a archosaur-like animal, and the combination of the Dinosaur DNA with the trimmed chicken genome causes the dinosaur DNA to take over and build a dinosaur.
If I had my way and could write a Jurassic Park sequel, it would go like this:
Soft tissue in fossil bones has changed paleontology. Alan Grant and co. are leaders in this area of research do to their years of field experience.
Lewis Dodson is the bad guy who never got his chance. He was instrumental in the first two books, but gets 3 minutes of screen time in the first movie. He's sinister, greedy, selfish, and cares only for profit. He has no moral scruples, other than his desire to make a profit for himself. Use him as the antagonist for the 4th movie. He's never gotten over his loss at Nedry's Hands. He never really gave up cloning dinosaurs. He sees money in them. His company has been sequencing genomes, and he has focused on birds- domestic fowl, endangered species, you name it. He spends a long time waiting. Then he hears about soft tissue preservation in fossil bones- blood cells, proteins...could there be DNA? Perhaps he is tempted to sneak out some of Grant's specimens without permission...
Point is- not only could you clone dinosaurs with the soft tissue story line, but marine reptiles, too. Giant ichthyosaurs, mososaurs, plesiosaurs...there's a lot of scary stuff in the ancient sea! For the purpose of Sci Fi, anything that's fossilized could be fair game! There's a lot of cool, extinct animals out there, people. Big, scary extinct animals...
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