There is only one thing that I feel should be in a sequel. Something unexpected and never thought of before.
I personally have two plots that I would like to see. One of them is showing how not only the planet is changing, but also how the gang is. Both physically and mentally. It would be good to see how an argument could destroy their friendship, and then a life-threatening situation resulting from that argument would bring them together again.
Another plot I would like to see is one that a villain takes advantage of a flaw in one of the five's beliefs.
For Littlefoot, someone who abuses his trusting nature. He would not believe the rest of the gang because of his trust, and that it would take a lot of evidence to prove his trust wrong.
For Cera, someone who uses her pride to his/her advantage. She would be too proud to ask her friends for help.
For Petrie, someone who uses his fear to manipulate him. He would be too scared to not listen to the puppetmaster, and would not ask his friends to help out of fear.
For Ducky, someone who takes advantage of her gullibility and good-heartedness. She would be too believing to listen to her friends, if the villain has shown enough to her to make her think he/she is a good friend.