Is it possible to keep Mac App Store apps in the user application directory?
I do not know if there is such a possibility to have this as a default behavior but you could simply move the application to your user application directory or anywhere else.

Finder by default creates an alias when you drag an application out of the /Applications folder. However, if you hold down the "Command" key while dragging your applications, they will move to wherever you drag them.

If you want to go a geekier route, you can also use Terminal and execute this command:

sudo mv /Applications/your-application.app ~/Applications/


After promting for your login password everything is fine. Be sure to be administrator of your system.

This certainly works for me. I can use the application as usual and it receives all updates via the Mac App Store.