This text is intended to serve as a back story and reconciliation of the design changes in Dinosaurs between films. Namely the Raptors and Pteranodons.
To properly reconcile the films and the Dinosaur changes seen throughout, one must first realize what the Dinosaurs INGEN created really are.
The Dinosaurs of Jurassic Park are, quite simply, mutants.
They are made complete by combining the DNA of other creatures with the original Dinosaur DNA which results in the animals possesing features and attributes not found in their true-to-history counterparts. They have been tweaked and modified to be as close as possible to real Dinosaurs but they are still not 100% genuine.
I have added a few quotes, links and personal theories to help prove this largely un-realized fact.
First is a cut quote from the Jurassic Park novel which the films were based on, adding support that they were not true Dinosaurs, I have removed Hammond's lines and only added the relevant lines from Wu:
[QUOTE]Well not exactly. Wu said. He paced the living room, pointed to the monitors. I don't think we should kid ourselves. We haven't recreated the past here. The past is gone. It can never be recreated. What we have done is reconstruct the past - or at least a VERSION of the past. And I am saying we can make a better version.
Why not? Wu said. After all these animals are already MODIFIED. We've inserted genes to make them PATENTABLE, and to make them lysine dependent. And we've done everything we can to promote growth, and accelerate development into adulthood.
BUT THEY'RE NOT REAL NOW. Wu said. That's what I'm trying to tell you. THERE ISN'T ANY REALITY HERE. He shrugged helplessly. He could see he wasn't getting through. Hammond had never been interested in technical details, and the essence of the argument was technical. How could he explain to Hammond about the reality of DNA drop outs, the patches, the gaps in the sequence that Wu had been obliged to fill in, making the best guesses he could, but still, making guesses. The DNA of the Dinosaurs was like old photographs that had been retouched, basically the same as the original but in some places repaired and clarified, and as a result...[/QUOTE]
Here are a couple of tidbits to add further support for this theory as well:
Alan Grant in JP3 stated the Dinosaurs of Jurassic Park were genetically engineered theme park monsters, nothing more, nothing less.
In 'The making of Jurassic Park' it is confirmed that the Dinosaurs are genetic mutants to a degree. See: http://www.youtube.com/watch?v=P9bKxRQfvs8 at 12:40-52
It is also a no-brainer that adding extra genes for patenting purposes, forcing quick growth, pumping them with vaccinations and the DNA of different species was bound to cause changes. Probably the best and most well-known example of mutation was the Frog DNA which caused the ability for some of the animals to change sex in a single sex environment. The Raptors in Jurassic Park had done this undetected and bred before they were transferred to their quarantine pen.
Also note there were two different versions of Velociraptors in the original JP novel. There were the captive bred version that displayed different colours, behaviour etc. and an unknown, wild born version which was migratory, seemingly less psychotic from being caged and had the additional ability to change the colour of it's skin.
In the films there are also two versions of Raptor. The original version was oddly enough first seen in JP3. This version was kept exclusively on Isla Sorna as they proved far too advanced and dangerous for a park setting. The second, which featured in the first and second films, was a modified version of the original, failed version. This version was created to be less dangerous and intelligent so it could be safely bred and displayed in Jurassic Park on Isla Nublar. However that version too was underestimated in the end and proved just as deadly but also even more hostile than it's predecessors. They would kill each other and attack the electrified fences to get at the feeders on a regular basis. The surviving Raptors of that generation were then quarantined in a holding pen while further research into a safe version continued in the Jurassic Park Labs on Nublar. Finally, when the Jurassic Park incident occured, further modifications were abandoned and as a result, there is currently no park-safe Raptor belonging to either INGEN or the succeeding Masrani corporation which has set out to succeed where John Hammond and INGEN failed.
The Pteranodon is another species that was a failure in the beginning. INGEN succeeded in recreating a species of Pteranodon with the intention of adding it as a future attraction to Jurassic Park. The animal was kept in a massive aviary on Site B. At first, it showed only a minor mutation in the form of teeth but this was considered completely acceptable, after all, many other species like the Dilophosaur had already shown varying mutations deemed acceptable by INGEN. However it was later discovered that they were highly territorial and migratory. They simply couldn't be safely managed in a Park setting. So INGEN set out to revise the species. They wanted it smaller and non-migratory. They eventually succeeded and this is the version seen at the end of The Lost World.
When the Hurricane struck the Island and destroyed the facilities there, all the animals were set free to fend for themselves by order of John Hammond. All but the first version of the Pteranodon. Being migratory, they could not be released with the others as they would surely leave the Island and find new places to call home thus causing a massive headache for INGEN, so they were kept caged on Sorna in the hope they would simply die out.
The two Raptor versions kept away from each other and formed separate tribes in different areas of the Island.