I just installed Lion, and downloaded Xcode 4.1 from the Mac App Store. I like having my Xcodes installed in /Developer directories that have their Xcode versions appended (e.g. /Developer-xcode3.2.6). Downloading Xcode 4.1 from the Mac App Store just gives me an installer app, which does not allow me to specify an installation location, as Xcode installers did in the past. When I ran the installer, it asked me to move old Xcode 3 installs out of /Developer, so is just renaming the /Developer directory sufficient? Will that break stuff?
Locate the 'Xcode Install' package. Show package contents. Inside the Resources folder you will find Xcode.mpkg. Install as usual.