Because they don't have enough room. The Mummy/Kong show building is huge...when Kong was in there, it was a short and simple loop layout, even with all that space available. To do a King Kong ride justice, you need big sets. The Disaster building doesn't have the luxury of a lot of room. And when you consider that the HE blocks any possible expansion opportunity, you realize that what's in Disaster now is pretty much all you're gonna get as far as physical sets--that leaves no room for the large scale effects and sets that were present in the original Kongfrontation which took up the entire Mummy building.
To achieve the scale of a good Kong ride while still effective,y utilizing the relatively small Disaster building, 3-D is pretty much Universal's only option.
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I don't think Shrek is going anywhere anytime soon--it's still the chief attraction used in marketing The Studios (similar to Potter or Spider-Man for IOA), and one of the only family properties present in Universal. And he's still popular to most people who dont realize how poorly-done the show actually is