CoP is great! My kids (5,7,9) even wanted to do it more than once last trip. I am 34, and I think we are probably just starting to hit full stride with the "WDW Nostalgia" thing. People who got to go to WDW when they were young (7-16yrs old, maybe?) some 20-ish years ago now have their own families and want to share that initial feeling of wonder and excitement with their own kids. That may be one reason why we are starting to see some of the old "style" of Epcot return. Besides possibly realizing that it was BETTER architecturally (and other ways, in my opinion), I'm sure that people in management, marketing, etc. see this trend out there...
If you think I'm smoking something, just look at some of the recent movies: Transformers, GI Joe, Inspector Gadget, Speed Racer (ugh), etc.. All of these things were popular in their 'original' form when I was young (late 70s, early 80s--same time as the opening of MK and Epcot, right?). The parks have been around long enough now that there is only going to be more and more nostalgia associated with them... which means that it may become more difficult for WDW management to decide what stays and what goes...
Personally, I LOVED Swiss Family Robinson (the movie) as a kid, but the treehouse (especially WITH kids) just seems like drudgery. It's a climb up stairs when you're already tired--for next to nothing! You can't touch things, you don't ride things...
Have not been to Tom's Island, but I don't really see why kids would need to know who Tom IS to enjoy the island. It may deepen their appreciation, but I don't think it is necessary. Hope to make it there this Dec.
I think a successful park will keep some classic attractions (CoP, e.g.)--especially if they don't take up that much space (Jungle Cruise would be a good example of a "tired" attraction that takes up a lot of space)--while also introducing new attractions (that, ideally, would inspire the next generation and, in 20 years, will be the nostalgia that they want to introduce their own kids to).
So, getting back to the OP, if I had to pick one, I'd say refurb/remove the treehouse, BUT I think there are much better 'targets' out there than the three mentioned in the original post...