This is a cool idea for a thread! I agree with just about everything OP suggested.
I could probably think of more changes I'd make but here's three that comes to mind:
Rooter
I could probably think of some more later but the one that really comes to mind is Rooter, the friendly Scolosaurus Littlefoot bumps into (literally) after losing his mother. He seems to be a kind and caring dinosaur, yet it doesn't seem to occur to him to help this recently orphaned, starving child?
I know dinosaurs at the time mostly just cared about themselves but even so, it doesn't make much sense to me. It sorta lessens the impact of that scene a little bit.
The fix would be simple. Just make him some semi-aquatic species, and show him swimming off before giving Littlefoot some important advice. That would have indicated to the audience that Rooter couldn't have followed Littlefoot on his journey.
Greedy longnecks
In the scene where the gang discovers a lone cluster of trees, only to see it abruptly depleted by a herd of apatosaurus, I would have changed them to some non-longneck herbivore. Iguanas maybe. I'd also have them crush trees and fight over the remaining treestars. It would make the scene more intense, give the kids a reason to just stay behind as they do and really shows the desperate, dire state of the world.
Plus, if they were longnecks, it introduces the question of why Littlefoot just couldn't go with them. Surely, they'd accept one of their own? Besides, I think the story works better if Littlefoots mother and grandparents are the only longnecks he sees before reaching the valley.
Domeheads => Raptors
I would have also swapped out the domehead Pachycephalosauruses to some raptor species. A. because raptors are cool, and B: it just makes more sense. It'd also have an establishing shot of the raptors hiding behind some rocks or something as the gang reach the tarpits.
The original scriptb]
Just about every deleted scene I've read and heard of from the original script seems like they would have improved the story. Especially Littlefoot finding the valley before going back to tell his friends. It just works better that way.