Hi,
I know that dropping .emacs altogether might be radical. I was trying to tease in order to start a discussion.
However, my point is that currently, if you want to have a separate custom file, all you have do is to set and load the custom-file in your init.el
I have this at the end of my init-el (as I think many have)
;;
;; Customisations
;;
(setq custom-file (locate-user-emacs-file "custom.el"))
(load custom-file 'noerror)
What I propose is to agree on a default value for custom-file that could potentially be changed by the user in init.el or .emacs
and do the (load custom-file 'noerror) after loading the init file as a default behaviour for Emacs
Having a separate customisation file by default can ease debugging, resetting customisations, bookkeeping, etc. etc.
/PA