Dukeis #1, the reason that the boats closed is that many people thought that the boats were a great attraction/efficient form of transportation/anything worth riding. They were none of these. However, there were really long lines of hopeful guests, who became very dissappointed guests after getting off of this short, one-way attraction. The exit surveys were dismal. But I do agree that the park could have been designed to be more travel-friendly.
As for full-fledged Imagineering screw-ups, I really can't think of too many that were completely WDI's fault. More often than not, there was some other factor, such as budget, causing them to design something the way they did. However, I do disagree with the entire idea of Dinorama, that has no place at a Disney theme park. I remember walking through Universal and seeing the cheap carnival games near Jaws. I was immediately relieved to think that I'd never see anything of the sort at a Disney park. Little did I know...