Easily The Lost World. It's simply a better made film. I don't think Jurassic Park 3 is as bad as some people here, but The Lost World has a stronger sense of wonder and scale. The action scenes are directed more competently and, unlike Jurassic Park 3, there doesn't always have to be a dinosaur on-screen to evoke a sense of danger.
It's a little long in the tooth, but Spielberg makes up for that by book ending slow sequences with interesting and exciting scenes. And Malcolm made an excellent lead character.
The Lost World all the way.
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