That's the only unplugged weakness that's still severe on the iPhone/iTouch. Installing app updates, or removing and re-installing apps (intentionally, or by a sync issue) more often that not wipes your data – annoying if it's game progress rather than login details. On a hookie firmware you can install AppBackup which selectively backups up and restores app data, which is well handy. Shouldn't be necessary though, and wouldn't be if the data to backup wasn't contained within the .app container – it should be in a user directory instead. Remove an app, you remove the data.