It’s not so much an issue that the Prezi is online, but rather which site it’s hosted at. Many companies (the one I work for part-time included) have a desire to create presentations that may include sensitive company operating data, be it workflows, process maps, earnings statements, etc. As such, companies such as mine are wary of even using the online editor for the creation of a presentation, as some of that data, while perfectly secure for the time being, has the potential to be “hacked” by a third party. Simply posting the information outside of a firewalled environment is a concern for a publicly traded company.
Therefore, a way to generate Prezis offline (with Prezi Desktop) and then export them as the same .swf files that are already made on Prezi’s site would be ideal. From there, the plug-in really just serves as a Flash wrapper, guaranteeing that the .swf is shown with the proper navigation controls.
I’ve already talked a bit about how the .exe file that’s currently created isn’t much use at a self-hosted web level (in that you can’t embed .exe files, and can’t have them reference necessary resources), but a self-contained .swf that can be referenced as an attachment would be wonderful.