The Lost World always felt off to me, even when I was a kid. I think realistically, it was Universal/Spielberg trying to pump the gas and capitalize on the success on the previous one. They famously started production on the film before the book it was based on was even published—a book that they kinda had to convince Crichton to write.

As a result, I think there's a clumsiness about it. Thematically, it kinda retreads notions about pushing science too far and the exploitation of nature, and mostly pushes safari-type imagery as the major change. Plus the ending, which seemed like Spielberg wanting to do King Kong but with a dinosaur.

It doesn't really try to say anything new, characters keep doing silly things to drive the action (Harding scolds the other characters for using water on a fire since it'll attract predators, then brings a baby T-rex back to the camp, and leaves bloody rags hanging in the open... both of which get people killed), and the third act does feel really disconnected. Like you said, a lot of the characters disappear and it doesn't even bother to really explain how the ship's entire crew died without any real damage being shown, and somehow it was still able to arrive at the dock it was destined for somehow... I dunno. The story was a justification to brute force a lot of big set pieces, which is ultimately fine because they're Spielberg set pieces. JP3, at the very least, kinda overtly telegraphed that it was mostly there to deliver on crazy dinosaur action, which worked for me quite a bit.