Again? How about not being bothered the first time? It sounds like `package-initialize' is evaluated the first time, unconditionally.
And it sounds like, even if I don't use the package system, I will have to edit a secondary init file (the first one read), just to tell package.el "Hands off!" And if I want to try a package in a particular Emacs session then I need to once again edit that first ("secondary") init file, to enable the package system. Is that right?
It's hard to believe this has to be so convoluted. (But I understand that you are saying that what you propose is less convoluted than what we have now.)
It seems to me that use of package.el should be just like use of any other library. Users should explicitly opt in. But I understand that you've said that it has been decided to enable the package system by default for everyone, at the outset.
That seems like a mistake, to me. And the only argument I have noticed in favor of it is that some users make mistakes and get confused. For that, I'd say start by improving the doc and making things as simple as possible for them - but without the automatic turn-it-all-on-for-everyone approach.
Users are not idiots. We all make mistakes and get confused. If the doc is poor and that is a source of confusion then that is the first thing to fix. If we need to simplify a few things, then it should be done. If it would help to add tutorials or videos then that could be done.
It should not be the end of the world for a user (apparently the typical Emacs user) to tell Emacs to activate the package system, i.e., opt in. It doesn't matter, IMO, if 99% of the users want to opt in; it should still be opt-in.