Depends if you want the typical corporate response, or a more realistic one.
The company statement is always something like "Disneyland was never meant to turn into a museum, and we are always looking at making room for brand new and exciting attractions."
However since the reality is it's set empty for over 5 years, I'm quite confident they did not close it with the intent of installing a new attraction immidiately. In fact they were a little over-confident of their "New Tomorrowland" and thought it would be such a success with a new thrill attraction Rocket Rods, that they didn't think anybody would miss the submarines, and closed them the year before the new Tomorrowland opened.
There have been rumors that range from a Little Mermaid attraction, then it switched to rumors of an Atlantis based attraction, and the current rumors are that it would be based on the upcoming "Finding Nemo" release scheduled for a theater release next year, which is going to be Pixar's newest offering.
Since attractions take a couple years, and nothing has been officially announced, I would not hold by breath for a replacement attraction anytime soon, although I'm sure one day it will, but probably not until after the 50th.