Here's what I think Disney's "Dinosaur would be like if the species were more accurate for what was alive at the end of the Cretaceous period. Here's the following changes:
Iguanodon- Triceratops. I was considering going for Edmontosaurus, but considering that an old concept by Phil Tippett had Styracosaurus as the main character, I thought, "Yeah, what the heck?"
Carnotaurus- Tyrannosaurus rex. That's a no brainer.
Styracosaurus- Edmontosaurus- If I remember right, there was going to be an Iguanodon filling the role that Eema had in the final film, so I went with Edmontosaurus.
Brachiosaurus- Alamosaurus- I guess it didn't occur to the writers that sauropods, more specifically, titanosaurs, like Alamosaurus, were alive at the end of the Cretaceous
Lemurs- Purgatorius- For me, they're the closest creatures the Late Cretaceous had to lemurs.
Ankylosaurus- Unchanged, apart from the anatomy.
Parasaurolophus- lumped in with Edmontosaurus. Because we have no solid evidence of Lambeosaurine hadrosaurs in the latest Cretaceous, I decided to stick with Edmontosaurus instead.
Pachyrhinosaurus- Lumped in with Triceratops. I was going to go with Torosaurus, but felt that it was too similar to Triceratops
Stygimoloch- Pachycephalosaurus- modern research suggests that Stygimoloch is now a growth stage of Pachycephalosaurus
Struthiomimus- Ornithomimus
Microceratus- Trierarchuncus- I'm just going to refer to them as Alvarezsaurs, because the official genus name is such a pain to pronounce.
Oviraptor-Anzu
Pteranodon- Quetzalcoatlus
Koolasuchus- speculative giant salamander
Ichthyornis- speculative seabird