Since this film is basically a Looney Tunes style of cartoony, here's the my list:
1. Changing the Apatosaurus's head design so that it does not look like this

when in front view.
2. Lengthening and making the creatures' tails skinnier. That has seriously been bugging me as they look foolish with those tails and recently, I thought that if dinosaurs had obese tails in real life, they would automatically have a tripod stance due to their tails' weight.
3. Changing the creatures' facial features so that they don't have tubular nostrils and heads shaped like a block from Minecraft.
4. Removing most of the creatures' skin sleeves. For crying out loud, not almost every creature needs skin sleeves!
4. Removing all the fat from the Saurolophus' nose and making Mama Swimmer a lot more feminine than looking like her husband.
5. Making the designs less cartoony and more like that of The Secret of NIMH except for the Dimorphodons and bugs.
6. Removing the scene where Petrie's eyeballs bulge out. For goodness sake, this makes this film a lot more comedic than dramatic.
7. Making Sharptooth more intimidating and making him look like the one from the poster.
8. Improving the sound quality. The sound quality is so bad in the first film that sometimes, I could hardly hear the characters talking or making other noises.
9. Making the children a lot more similar to their parents. They are so different, with the exception of Petrie, that I decided that they are a different variation from their parents.
10. Giving the words "Sun" and "Earthquake" their proper names.
11. Giving Topps, Mama Flyer, Mama Swimmer, and Littlefoot's grandparents far more dialogue.
12. Removing any bit of racism from the film. I'm not sure how a film with so much racism can get fantastic reviews and a G rating.
13. Making this film far more of a drama like Secret of NIMH than make this film more for little kids and toddlers than adults.
14. Making the kids more comparable in size to their parents. I never really get why Ducky looks like an an compared to her mother.
15. Making the flyers eat bugs rather than leaves.
16. Making Sharptooth's roar a lot more audible. Either his roar is far too quiet or I'm just a pathetic loser who somehow can't hear Sharptooth's roar and need to get my ears checked.
17. Giving the juvenile Triceratops brow horns.
18. Do something so that the characters' mouthes don't open at ridiculous gapes.
19. Making the characters less childish and more mature.
20. Improve the characters' facial expressions. The fact that sometimes, characters look like their smiling, even when they're not supposed to be, enrages me.
21. Stiffening Ducky and Petrie's crests and not have them flop around like spaghetti.
22. Adding a scene where Petrie is born.
23. Removing any part where Cera's voice breaks and therefore sounds like a man.
24. Making the quadrupedal dinosaurs limbs erect rather than sprawling as that concept is far too outdated and was thought to be innaccurate even before 1988.
25. Removing the dinosaurs' mammal-like ears.
26. Give the characters when their in the Great Valley their true colors.
27. Doing something so that Cera always has girly eyelashes and not just sometimes.
28. Removing the fleshy ridges on the dinosaurs' backs except for Saurolophus and T. Rex.
29. Giving the Ornithomimus a more ostrich like face than an eagle like face.
That's all I can think of for now.