I'll give my opinion on each choice:
Castle as a Cake - I didn't hate this one bit. I enjoyed it for the time it was there. The key was, it was just there for the 25th celebration and didn't over stay it's welcome. This would be dead last on the bad decision list for me.
Epcot/Spaceship Earth Wand - Middle of the pack choice. I didn't mind it for the Millennium Celebration, but it DID overstay its welcome in a big way. But it could still be up.
The Seas with Nemo and Friends - Right ahead of the Castle Cake. I hate the over characterization of the parks/new attractions, but this one actually makes sense. They could have made the ride portion more educational with the Nemo characters instead of giving us a poor man's Submarine Voyage from Disneyland, but it isn't bad.
Cancelling Tapestry of Nations Parade - Right ahead of Seas. I thought this parade was "OK" and was fine for the Celebration, but I don't miss it.
Stitch's Great Escape - Easy choice as the worst decision ever. For me, it replaced the greatest attraction in WDW for the single worst attraction in WDW history. Enough said.
Closing of Mr. Toads Wild Ride - Probably the 3rd choice. I love my new Toad shirt that I bought yesterday at the MK and I do miss the attraction, but it wasn't the best thing in the MK and Pooh is alright.
Closing of Horizons - 2nd choice for me. This was the best attraction in Epcot history, no doubt about it. An update to the attraction would have been perfect, but they really messed up by tearing it down. With that said, I love Mission Space. I appreciate its creativity and originality and enjoy the ride experience.
Stitch's Supersonic Celebration - Pretty big mistake because they are barely getting a month and a half out of all that work, but at least it is leaving. I think the American Idol Experience was a bigger waste of money though. That attraction is a definite "one and done" for me.