Xcode 4.6 not installing on my Mountain Lion
You can download the DMG separately this time. You do not have to go through the App store, but it requires a free Developer account. 

1) Log into the Mac Developer Center
2) Scroll down to the "Xcode 4.6" section.
3) On the right there is a button to download Xcode 4.
4) Open the DMG.
5) Drag the old Xcode from the Applications folder to the Trash.
6) Drag the new Xcode from the mounted volume to the Applications folder.


This time it will download a DMG file instead of a link to the Mac App Store.

Either way you will have to download reinstall any extras from within Xcode itself. See the Preferences -> Downloads tab to finish the install.