I think that the CGI at night and in dark locations still holds up really well but the stuff in the broad daylight does show its age now. Bear in mind though that JP was far ahead of anything else at the time in terms of CGI.
The problem is that it's so prevalent now that it's a case of 'shoot it quickly and we'll fix it in post'. At the time of JP that wasn't a choice, CG took so long to do that you couldn't spend time tweaking everything, you had to be pretty certain you did everything right on set. Plus don't forget that their was only 6 minutes of dinosaur CG in the first film so there wasn't the same amount for people to be able to pick through.
The couple of bits I was really impressed with, which I found out after a few years was that when the kids were in the car getting crushed by the T-rex they were actually composited in there afterwards and also the head replacement when Lex fell through the air vent.