Basically, I think the whole V-rex fight could be shortened. Granted, it's was nicely done, but it goes on for so long that you start to question the plausibility. They fight, fall, hang, then fight again. Yes, Mr. Jackson, seeing him fight three at a time is cool and all, but it eventually becomes just a showcase for the effects.
I'd also trim the bug scene a bit. I didn't find the whole 'shooting them off with a machine gun' entirely believable, but I'm not sure how else it could be handled. I get that he's going for a thirties like film with overthetop action, but it does get carried away.
The dino chase also gets a bit muddled towards the end.
Also, I'd either shorten or remove the Venture pan shots. The dynamic camera really gives away the effects.
If it were up to my sister, she'd cut the ending. ^_^
All in all, not much should have to be done, as it's a great film. A little tightening in the action department should be all it needs.