Okay, so my theory is that they hired a demolition crew and they're just going at it all at once to save money... the skyway station, the lagoon, the tomorrowland stage, it's a small world.... all sorts of tearing down all at once. Besides, 20k has been dormant for so long, it was getting harder and harder to mask the effects of a dormant body of water on the theming and old unused ride system. As a result, I'd totally expect them to bring back the character meet and greet that had been in the queue line for the last several years, only without the worry of a big body of water rotting away. They may build in something eventually, but I wouldn't expect that management is that keen on putting out the money for construction costs quite yet.
As for your Finding Nemo dream, Disney is going to need to start distancing itself from long term pixar related projects and they already have finding nemo theming over in Epcot at the Living Seas. It seems pretty save to assume that with the removal of the lagoon, those old hopes for a Nemo or even Atlantis themed ride are probably shot, in favor of something drier and cheaper to upkeep.
Jack