Baryonyx, a close relative of Spinosaurus, was considered in place of the Spinosaurus, during the early pre-production phase of Jurassic Park III. Spinosaurus was ultimately chosen, as it was bigger and more impressive with such a sail.
At the beginning of the movie, there was supposed to be a paleontologist in Egypt uncovering a Spinosaurus tooth. This scene was likely removed for being insignificant to the film's plot.
Ben Hildebrand's death
Paul and Amanda Kirby
Ellie and Grant farewells
A scene, that many fans feel should have been kept, was a longer goodbye between Alan and Ellie. There was also another scene in the dining room where Jack the Parrot responds with "Bullshit!" when Ellie and Alan are discussing the Velociraptor pack communication theory.
This scene was included in the movie trailers for Jurassic Park III. It was the plane taking off at sunset possibly from Montana to go to California for the Kirby's staging to proceed to go to Isla Sorna.
Nash and Udesky deaths
According to the original script, Udesky was going to be killed by Spinosaurus and Nash would've been killed by Velociraptors. However, their roles were changed in the final cut.
'Alternate Spinosaurus vs. Tyrannosaurus rex
Originally, the sequence between the Spinosaurus and Tyrannosaurus rex involved a short moment where the two beasts sized each other up, while roaring and growling. The conflict would be started by the Spinosaurus, who smacks the T. rex across the face, rather than the T. rex making the first strike. This sequence can still be seen in trailers, and also in the special features of Jurassic Park III. Additionally, The Making of Jurassic Park III shows an extended sequence of fighting where the T. rex begins to push the Spinosaurus back and an Extended shot of when the Spinosaurus bites deeply into the Tyrannosaurs neck. Only half the scene remains in the film. The original fight was 2:18 long and the final is only 1:09 long.
"'Alternate You should come look at this!"
This is simply an alternate take on the "You should come look at this!" line in the film, seen in the trailer for III.
When Udesky threw off his backpack and fled into the forest, he fell over, got up, and heard the sounds of Velociraptors. This small sequence was removed for pacing concerns.
The red Velociraptor
There was supposed to be a red Raptor, but it was never used.
Udesky vs. Velociraptors
Udesky, in a cut scene, attempts to use a stick to hit the Velociraptors to defend himself, with the Velociraptors overpowering and injuring him. In the film today, it just cuts to the raptors killing Udesky.This sequence can be seen in production stills for the film. The scene was also possibly finished.
When the crew entered the lab, Paul was supposed to see a broken coat hanger. It was taken out due to pacing.
As Dr. Grant, the Kirbys, Billy Brennan, and Udesky go into the Embryonics Administration these scenes were supposed to extend it likely to be longer showing a bit more depth and how large the structure was, as well as the weapons from the first film. It's implied these sequences would've pushed the narrative of Sorna being a research facility.
According to the official shooting script, there was supposed to have been a scene where Eric is in the compound and notices freshly made footprints.
Velociraptor motorcycle chase
There was going to be a scene, which would have involved Alan Grant driving a motorcycle in a greenhouse like building while velociraptors chasing him, however this scene didn't make it to the film.
Billy Brennan's death
Originally, Billy Brennan was supposed to die in the bird cage scene, but the crew decided to save him for the ending.
This is an uncompleted effects shot of the Ankylosaurus crossing the river in front of the InGen Barge in the river bank scene.
Velociraptor vs. Ankylosaurus
At one point, a scene was planned involving the Ankylosaurs battling against the Velociraptors. This Scene took place after they found the abandoned lab.
Alternate Spinosaurus emergence
The Spinosaurus entry in the river raft sequence was different, originally, with the Spinosaurus making a rather explosive entrance.
Another scene, that was removed concurrently, was Paul Kirby's line of him "can't help from feeling a little bit offended" following the Ceratosaurus leaving the group alone after engaging everybody in the group who dug through piles of Spinosaurus droppings for the satellite phone.
Alternate Giving of the eggs
Originally only Grant and Eric were to give the stolen eggs back to the Velociraptor pack.
Paul and Amanda rekindled
This scene was believed to show Paul and Amanda rekindling following their rescue. Originally, this scene there was supposed to also contain or lead into a conflict with the Pteranodons and the Velociraptors.
According to an early script, around the time of this sequence, the speed boat incident's cause in the beginning of the film was revealed to be the fault of the aggressive Pteranodons. This sequence was cut, most likely due to a contradiction of continuity, as they were still locked up in the aviary at the time of these events.
Following this, Grant was supposed to thank Ellie for sending the rescue at the end of the scene, but this sequence was cut as well.
Actor Sam Neill said himself in an interview that there would be a sequence where a Velociraptor "interacts" with the Pteranodons. Rumors about this cut scene state that they would supposedly fight but the sequence never made it to the final product.
Two different versions of the film's ending exist in script format, where the Pteranodons attempt to attack the group while respectively inside and outside of the rescue helicopters, falsely assuming they are a predator.
Another variation of the ending in the original script had the Spinosaurus being killed off by a pack of Velociraptors after it attacks the group on the raft. Finally, a second alternate ending was of the Spinosaurus attacking the Marines/Navy after the group left the island, which ended up being removed due to pacing. Due to the scenes removal, it left the audience wondering what happened to the Spinosaurus.