Dear all,
I'm not an emacs developer, but one thing which wasn't brought up in this discussion so far is the following:
The entry in custom-set-variables changes continuously even if no new packages are installed, mainly whenever you update the packages: That will perform an uninstall of the old package and re-install of the same package with the new version. I don't change the list of installed packages often, but I do update my packages frequently and every time my .emacs changes. I find this annoying since I keep the .emacs file under version control.