If Skull Island is indeed a different design than PJ's Kong, I find it odd they'd go with the 2005 design. I mean, I know they have a useable set of 3-D film for part of the ride, so it may just be a cost saving thing, but you'd figure they'd want some semblance of cross promotion.
Then again, maybe not enough of the new Skull Island design is done and they may make it a random mish mash.