Personally, here is how I would do it:
First off, the staff would get completely overhauled. I would try to bring back Don Bluth as director, and the staff would consist of animators who either grew up with or are passionate about the films. Maybe even both
Also, it would not be a musical, due to being a slightly more darker and serious movie than the rest of the sequels.
The tone, story and designs would be closer to the original, and Ruby would be removed altogether. Gonna keep Chomper though.
As for the plot, it would take place a couple years after the events of Journey of the Brave. The gang are now slightly older. The Earth has fallen into a near-apocalyptic state. Volcanoes erupt left and right, and meteor showers strike the Earth on a daily basis. One of the meteor showers just so happens to hit the Great Valley, destroying it beyond repair, and killing most of the dinosaurs in the process. The gang survives, but before they go, Littlefoot's grandfather tells them that there is a sanctuary inside of a cave on the other side of the continent. Apparently, other dinos have also visited it. He describes it as a "Second Great Valley" in case the original got destroyed. There, the gang can live out the rest of their lives and potentially repopulate the earth. The main five (plus Chomper) embark on their journey to the sanctuary. Along the way, tragic memories from their past challenge and even traumatize them. They either have to make it to the sanctuary, or die trying.
As you can see, it would be kind of a reverse version of the first movie. Be sure to give me feedback.
