To be honest, it is quite possible for a relationship to not exist between the two. When you think about it, Littlefoot and Ali had a really strong friendship with each other even though they only knew each other over the course of one movie and one TV episode. I think it is possible for Littlefoot to always see Ali as a really good friend, especially since he said they were friends immediately in LBT IV. If he wanted to start thinking of her otherwise, then when she returned he would have tried to have some alone time with her to reflect on what they had been through. Of course, the episode pretty much blew off that opportunity with the ridiculous plot, and I'm sure they could have had some alone time off screen, but then again he could have easily found a moment when Rhett was not around to talk to her. Even if he was there, Rhett was not portrayed as bully and therefore would most likely not push Littlefoot away. Now again, the fact that they are kids throughout the franchise can go against my argument, but at the same time it is possible for kids to develop crushes at young ages.
Now is it a good idea for the two to be in a relationship? This really depends on your personal opinion. Littlefoot and Ali would be an easy and obvious choice for a relationship, perhaps maybe too obvious. While part of me says that the events of LBT IV were good enough to create a foundation for a start to something, another part of me feels that this would be too cliche, even for LBT. Think about it. The only female longneck his age Littlefoot has ever met? It screams relationship, but it makes it too obvious at the same time.
So to answer the question, I am indifferent on a relationship between the two.