Surprised nobody has mentioned Kali. Every time it goes down for its annual refurb, it seems to come back with less working than before it closed.
EDIT: I'm in the camp that thinks Dinosaur is in much better shape than it was before the refurb, but I also agree with some of the OP's points. Many areas of the ride now seem to be too brightly lit, and the penultimate Carno encounter did seem a lot less intense than it previously was. For one, he was just standing there hanging out and pretty brightly lit before we even approached him, so any element of surprise or suspense was ruined. Additionally, the roar seemed much quieter than I remember, and he didn't seem to lunge at the vehicle as threateningly as he used to. He also seemed to be moved further back from the ride path, but that could just be my imagination. Also, didn't there used to be an air cannon that blasted you as he attacked? That definitely didn't happen either.