1-well I can think of one good excuse for JW, the t-rex is the exact SAME t-rex from the original park
so you can't just change them (especially not so suddenly).
2- it's a movie that is telling a story, not a documentary
(if you want a dino-movie to be like a documentary, make raptor-red into a movie)
besides, while your argument works with time-travel films (like "Primeval"), or films that actually take place IN PREHISTORY (like disney's "dinosaur")
it simply doesn't work for JP, they have a good reason to be that way, a reason that was stated in the novels.
if we were to clone dinosaurs (ignore how we'd do so) we wouldn't be able to get a "pure" dinosaur but instead, a "neo-dinosaur" that looks like how we engineer it.
because the truth is, WE DON'T KNOW 100% WHAT THEY LOOK LIKE!
(that and you have to allow some creativity)
so whatever you say, the JP dinosaur are like that because it is realistic in that context!
3- if you want, you could ask for movies (or documentaries) to have a disclaimer.