You are certainly right that a good leader would probably make his followers feel not like followers but like people acting on their own will and accord. One thing I must make clear is that I don't think of Littlefoot as a "bad" leader (though I may not like the term "leader" in general as it often indicates a hierarchical structure which can in some cases be abused). In any case I would not go so far as to call Littlefoot a natural born leader (though I think similar descriptions can be found in official sources).
In many cases Littlefoot is coming up with good plans or ideas and therefore it is kind of easy to "follow" him. If a good suggestion is being made it is relatively easy to make others act on it if the others too agree that it is a good idea to pursue that plan or idea. I guess leadership is displayed in particular if people are convinced of a course of action although there are alternatives which they might prefer. There are many such cases throughout LBT.
In LBT 2 Cera, Ducky, Petrie, and Spike are following Littlefoot looking for Chomper although they don't really want to. They don't really trust Chomper, they are hungry, they are tired, and Cera may be suffering from an aching bite in her tail. Littlefoot just goes on and does what he thinks is right, that is he tries to protect Chomper from any harm. Cera's protests are answered with a simple "No one is making you come!" and before Ducky's and Petrie's protests (they're hungry) can be responded to and before we see what effect Cera's suggestion ("Let's go home!") has on Ducky, Petrie, and Spike, Littlefoot spots Chomper thereby changing the status quo in such a manner as to make the others follow him. But is this really leadership on Littlefoot's part? Would the others have gone on if Chomper hadn't been spotted so conveniently?
Later on in the same movie Cera, Ducky, Petrie, and Spike
don't follow Littlefoot. When he is rushing to the aid of his grandpa they stay behind and reappear only when Littlefoot is already being pursued by a Sharptooth whom he and Chomper had tripped while common sense might have told them to hide (what advantage did they gain from tripping the Sharptooth?).
When after the defeat of Chomper's parents Littlefoot realizes Chomper is not around anymore he sets out on his own once again. It seems like their parents order had a greater power over them (even in the absence of their parents) than Littlefoot's setting out on his own.
In the same movie Littlefoot is sort of "overruled" by Cera on two occasions (that is Ducky, Petrie and Spike, and consequently Littlefoot) follow Cera's suggestion rather than Littlefoot's opposition. The first case is Cera's plan to cross the sinking sands and the second case is when she suggests to chase the eggeaters rather than telling the grownups about them. In both cases Littlefoot allows himself to be led by Cera (though he takes the helm during the pursuit of the eggeaters the initial idea was not his). Of course in both cases the group might have been better of if they had followed Littlefoot, but this says more about Littlefoot's sensibility rather than his leadership qualities.
In LBT 3 we have a case in which I think Littlefoot does display some good leadership by convincing the others to follow the bullies. Once again he gives that "You guys do what you want!" Statement, but following the song "Kids like us" I really think they were doing what they wanted. They did not follow Littlefoot just to protect him from harm. He led both by conviction and example in this case.
LBT 4 is not as explicit in statements about Littlefoot's leadership qualities. We have Spike making an important decision for Ducky and Petrie (to trust Ali) and we have Cera following them as well after all. Yet I suppose Cera's following them was more out of concern for the safety of Littlefoot and the others than for any leadership question.
LBT 5 gives many interesting examples again. Littlefoot comes up with the good idea of keeping the herd together by leaving it (sounds like a paradox

) and leaving good tracks behind. We hear Littlefoot laying out to Cera why they had to "walk like this" but I am not convinced of this explanation being an example of leadership as it was probable meant to be for the audience rather than for Cera. After Ducky and Petrie find themselves in a big sharptooth track we have Cera trying to calm them in her over-self-confident manner. Ducky means to leave (not wanting to
be food) and Littlefoot tries to convince her to stay. But just like in case of LBT 2 the discovery of the Big Water comes in very conveniently. We never learn whether or not Littlefoot would have managed to keep Ducky on the track.
Later on in the story the main question is whether or not to trust Chomper. Once again we never learn how this matter would have been settled had it not been for the attack of the sharptooth, Chomper's display of heroism and the "pacification" of his parents. Ducky, Petrie, and Spike seemed to share Cera's misgivings about Chomper but Littlefoot never ever showed any sign that at least he understood where their worries were coming from. He who understood why Petrie would be afraid to fly above the big water seemed to have absolutely no understanding for the fears of his friends about Chomper. What would have happened upon Littlefoot's return to "stinky place" had he not had the sharptooth on his heels? Look at the scene. Littlefoot returns worried about his last treestar, but Cera, Ducky, Petrie, and Spike come to meet him. I don't want to over-interpret the scene, but they really look like they meant to have a serious word with Littlefoot. Once again disaster strikes conveniently.
In LBT 6 Littlefoot gives a rather poor show as a leader. Perfectly incapable of understanding that the others may not be as taken with Doc or the lone dinosaur legend as he is he just sets out "on his own". The others come to the rescue ("don't we always?") but again more for their concern about Littlefoot than for any other reason. Ducky too shows some initiative in this movie. She is the first to hop over the rocky pillars (which corresponds rather strangely with her later display of panic at the idea of walking across the canyon over the log).
These are just some examples, but I guess they are something to begin with before we go on to the other sequels.