I would like that also, keeping all saved game data of every game/emulator in one folder would be nice. I also like the idea of a central rom folder, this way browsing your rom collection would be easier and there would never be any guessing where to put roms.
Two folders -- application and saved data.
A perfect program install is one that is contained solely in one folder, not scattered throughout the hard drive.
You should have the option to keep your saved data if you upgrade/uninstall, and you should be able to delete your saved data without breaking the application. Exactly what the pnd format provides!
This is different, actually. The way the PND format does it, is that each separate application would have it's own settings (or saved data) folder. There are way too many errors that could crop up by putting them all in the same folder. (such as save files for 2 different emulators requiring the same name)