I miss Mr. Toad. I miss Alien Encounter, too. I think people who say Mr. Toad and Alien Encounter were un-Disney are over-sensitive. To me, Alien Encounter was an amazing, cutting-edge attraction, totally unrelated to any Disney movie, just like some of the most famous Disney attractions ever designed (POTC, HM, Space Mountain, Jungle Cruise.)
I would love to see some new attractions un-related to Disney movies that use cutting edge technology, just like Alien Encounter, POTS, and HM when they were new. Anything in Disney is Disney, to me, as long as the show stands up to Disney standards. Some would argue the lack of continuity in Tomorrowland is un-Disney, too.