I just watched it again a couple hours ago, but my god do I hate Sara and Vince Vaughn's character and I believe much of the flaws boil down to those two and their actions.
I would argue it actually has loads of problems. The fact that the exposition phase for the existence of 'site B' takes about 15 minutes is a good indication of that. Even if you argued that it's the same length as the dig site invitation in the original, the structure of the original worked due to its massive self-reference structure. Literally everything in JP1 refers to something else in the park (the map we see constantly, and we see changing as the power goes off, for example) or about to happen (throwing away the raptor claw preceeds their release, the goat and the no-show foretell the paddock scene, and so on), whereas TLW has 'a map' but can't relate to it because it's not that kind of story.
As a result however, you get what seems a lot of loose ideas stringed together into the impression of coherence, but as anyone can tell by how awkward it is to have Roland at the cliff after the Rexes were just there (I noticed this as a teenager watching the movie in cinema's for the first time), then the inexplicable bones of bigger herbivores near the raptors (which are there in the novel due a river carrying them there, as tiny raptors could never move such large animals on their own), the general uselessness of the hunters, and the unexplained psychopath behavior of the raptors. That last one is actually the twist in the novel, but the movie, despite more exposition than is good for it, never explains why that is, thereby kind of 'missing the bloody point'.
But in all fairness some of these are problems stemming from the novel, which is very clearly Crighton taking a piss on himself, including a second Ian Malcolm morfine induced information dump, because clearly everybody just loves hearing some jackass ramble (really, that particular scene in the novel is super akward), and the fact that he was of course quite dead at the end of the first.
That doesn't however, excuse the explosion of the number of people on the island (the hunting party in the novel is three people, with five with malcolm), the san diego sequence (jacking it, jacking it, jacking it, jack... oh wait), and the gymnastics nonsense at the end. Spielberg's changes do however, give a nice exposition of species with the initial capture sequence. But we all know the rexes save this movie, yet that's also the problem: they are the only piece the movie can actually depend on, with the raptors playing second fiddle (though there are a number of technical shots there that few others can produce) without it being explained why that is.
I don't hate it or anything, but even at the time you just knew it couldn't quite get to where the first got us in terms of viewer emotions and the cohesive strength of the story.
If anything, that's why they returned to a park with this movie. Nobody wants to see another JP3. But a park works due to its nature of the illusion of safety through control, whereas senselessly going to an island with free dino's on it requires a leap of logic that most people wouldn't.
/ cents and nitpicking
edit: as a sidenote, Pete Postlethwaite's performance completely overpowers every other character.