At the moment there is no way to change the type. Note that new-style packaged apps aren't yet discoverable in the store. When that changes and end users are able to browse new-style packaged apps, there will also be a facility for updating legacy app types to the new type. Stay tuned!
Update 5/7/2013: Apps are now discoverable for users who are able to install and launch them through the App Launcher (Windows and ChromeOS users on dev channel). The type-switching feature isn't yet available, but this is actually a desirable situation because switching a popular app to a non-legacy app type would immediately reduce its visibility to that smaller set of users.