I think that point is critical to the adoption of these new technologies for presenting information. Architects have to adapt our presentation style to more contemporary practices in visual communication. The brilliance of Prezi is that one can negotiate between several scales and drawings types, allowing the relationship between these form intuitively with the client instead of trying to convey these relationships directly using conventional architectural annotation.
I for one hope for the day when we can begin to pull away from the 2d plane that Prezi provides and begin to discuss spatial geometry in 3d, while maintaining the interface benefits of Prezi style navigation.