Basic Changes: I think that Olmec would get new or extra lighting, maybe red or vermilion, and the set would look more aged. The "faces" on the columns beside the central shaft would be almost unrecgonizable, and parts of the small walls (like at the front of the Pit area) would be crumbled, representing age. Also, in S3, during the temple games explanation, the music would start in the middle of the track. I think they would make it like S2 again, where the Olmec's Advice track starts at its begining.
Opening Changes: I think that the camera would still move through the jungle, maybe some new wildlife sounds, rushing water sounds, and the viewpoint of Olmec when he comes into view would be different. They would have to make a new Kirk entrance, and the opening would still be pre-recorded.
Set Changes: More foilage, possibly a waterfall emptying out into the Moat and its other end carrying out the set in a stream. Some more plants near the moat. The gongs I think should be slightly mossed and their gold color should be slightly faded. The small smiling face should be removed from Olmec, it looks kind of dumb. The moat could have a deeper shade of blue, and the fog would still be there.
Temple Changes: I see them making rooms darker and possibly putting in more mist or disorienting features. I think that they would keep the Crypt, but replace or repaint the Ledges. They would keep the Pit of the Pendulum, The King's Storeroom, The Room of the Ancient Warriors, The Shrine, The Quicksand Bog, and the Tomb of the Headless Kings. They would probably get a new room for the bottom-third area, but it would have an objective besides hitting an actuator. The Dark Forest would be changed to something else--they've already had it for six layouts. The Room of the Secret Password could be changed to something else, ditto for the Chamber of the Sacred Markers.
Well, those are my thoughts.