A very interesting comment Michael and a view one can take. However, I disagree with the view that Ali didn't have any flaws in LBT 4.
Not being used to someone and therefore acting shy may not be a flaw, but in case of Ali it is not about being shy about someone for not being used to him or her. Having never ever seen or talked to Littlefoot before she introduced herself by biting his tail which doesn't exactly show a great degree of shyness about foreigners in general (come to think of it Littlefoot's reaction (especially thinking of his first contact with Shorty) could have been quite different

).
Ali's shyness bears a very distinct trace of racism / specism since it is not foreigners in general she fears but foreigners of other kinds (it might be compared to someone who doesn't want to get into contact with others because they have a different skin color). While one may debate the degree to which Ali personally is to be blamed for this (having grown up in a herd of longnecks only that obviously doesn't tolerate members from other species) it still remains a flaw of character.
With regard to her intention to sort of have Littlefoot for herself she is also not overly picking in her choice of methods making up excuses / lies and sort of blackmails Littlefoot into following her without the others by just rushing up. Not the attitude a character as perfect as you consider her would take.
And the whole trip too is based on a lie (or at least an intentional concealment of truth) on her part. Once again Littlefoot's reaction could have been quite different when she revealed that she has no clue where the nightflowers grow having never seen them (just imagine the flowers hadn't so distinctly lived up to their name; they might have passed them without even recognizing them).
It takes Littlefoot's being in mortal danger for Ali to leap over her shadow and talk to the others at which point the question may have to be considered why she then talked to Cera, Ducky, Petrie, and Spike rather than trying to get another grownup whose ability to clear away the rockslide might have been much more powerful. The main answer may be that it was necessary for the story so it would be kind of unfair to "blame" Ali for that, but still it remains not the action that a perfect character might take if the main point is to save Littlefoot's life.
So based on all that I cannot quite agree that Ali in LBT was a kind of Mary Sue character in special need of any additional flaws for lack of any.