Well, if this information is accurate I'm sad to see Cranium Command leave, but don't really care too much about the rest of it seeing as so much has been closed for so long there. As far as getting all the stuff for Body Wars out, it would really depend on how many modules they had and how many they were running when it was open. Theoretically, it's possible that if there were four modules, they could have removed two during times that the pavillion was closed previously and then only had to worry about removing the majority of parts for the last two. Technically, all they would have to do for it to be officially "gone" though would be to remove all the parts that make it operational, such as the doors, projectors, screens, etc. If those were taken out and not replaced, then that would constitute the same as it being gone.
As far as UoE/EEA goes, I doubt they are getting rid of the energy pavillion, but probably updating it. When you think of the things that have been developed over the past 10 years, hybrid cars being a great example, there is alot more that can be discussed regarding energy. According to reports, the Chinese are testing a fusion reactor later this year as well. Things like this added in would make an even more interesting and educational experience. The movie could always be updated and some of the rooms(like the radio tower room) could be changed to incorporate some of the newer technologies instead.
And besides, Alex Trebek doesn't have a mustache anymore...
Edit: For the article about the Chinese Fusion Reactor, go here:
http://www.angolapress-angop.ao/noticia-e.asp?ID=409853