It’s not only the lack of Organizer that makes the Mac App Store version of Elements 9 different. In order to comply with the App Store rules about installation and updates, the App Store version of Elements 9 has completely different file paths.
The things that Elements normally strews all over your hard drive are all contained within the app itself in this version. So, for instance, say you need to move TWAIN.plugin from the Optional Plug-ins->ImportModules folder into the regular Plug-ins->ImportModules folder so that you can scan into Elements.
You can look around in your Applications folder till your eyes ache and you won’t find anything. Instead, if you right click the PSE 9 Editor itself and choose Show Package Contents->Contents, you’ll find all those folders hiding in there:
So far so good. But when you try to move TWAIN.plugin, you’re going to see this unfriendly message:
Don’t let it put you off. Just click Authenticate, and you’ll be asked for your OS X account password and then you can successfully move the file. Oddly, you can delete files in here without authentication.
However, there’s one very serious problem with the App Store version of Elements 9. It doesn’t care bediddly about the file mediaDatabase.db3. If you like to install extra stuff into Elements, like layer styles, actions for the Effects panel, and so on, it just doesn’t work here. Anything that requires forcing Elements to regenerate this file is a complete no-go, since after you delete it, Elements runs just fine without it and sees no need to recreate it. This means the only way to run actions is from the Actions Player in Guided Edit (look in the folder Contents->Application Data for the things you’d normally find in Hard Drive->Library->Application Support). You can’t install anything into the Effects or Contents panels, so no add-on tools, no layer styles, etc. Brushes aren’t affected by this, but Smart Brush presets you make yourself are.
For that reason, I’d recommend sticking with the other versions of Elements (boxed or Adobe download) until Adobe fixes this, if you haven’t yet bought Elements 9.