I have to agree. It would have been pretty easy to make them darker.
as you say with number 5, it seems like a pretty serious, almost dark movie, until they run into Chomper. After that, it's clearly kiddy.
And as you say, if they had delved a bit deeper into Chomper and his thoughts, it could have been pretty serious. As far as I can tell from the real version, there is only one brief time when we get a glimpse at him struggling with his carnivorous nature (when he is apparently tempted to take a bit out of Littlefoot's leg). So, if his conflict had been the main conflict of the second act, it could have been a pretty serious film.
Another way they could have made it a bit darker is very simple: have the villains actually DO something villainous! When you think about it, most of the time the villain's evil is simply threatening. There are only a few times when the villains actually do something (such as when Pterano kidnaps Ducky, or when Dil almost devours her). A prime example is Hyp Nod and Mutt. Outside of threaten the kids, they do very little that is villainous. In fact, in number III, Topsy is almost more of a villain than them, with the way he tries to maintain order in the valley by taking control. If they had concentrated more on him instead of the bullies, he could have become the antagonist, and that would have been really interesting.
A few other examples of ways are the following:
As opposed to having the characters always narrowly avoid injury, or shrug it off in seconds, actually injure them a few times! I'm not talking copious blood or anything (though that would up the darkness a considerabel notch), just...you know, have character actually react to being injured, like limping, passing out, etc.
A simple change of the colour scheme. The first sequels were okay with their colour schemes, though they could do with making the pallette a bit darker. But the computer sequels (7 and onwards) were very brightly coloured, which makes them really stand out. If they just kept with the earth-colours/pastelle palette of the original sequels, it could have worked really well (In fact, I'd go so far as to say that this is a prominent reason that most people say that they thought the first few sequels were good, but the rest sucked). One thing they do get right though, is the colour changes for mood: such as reddening during a dramatic violent scene, or suchlike. Of course, this can be overdone (The Pagemaster is a good example), but if they used it more, it would certainly make them more imposing and dramatic.
Another easy example is the songs. You can basically separate the songs into 2 categories: The ballads and the sillies. (with a few exceptions). If they had just made a few more serious songs, that weren't ballads, maybe fans would have taken the songs more seriously.
I'm sure I'll think of more ideas, but I'll turn it over to you guys