Some ideas:
3. It would be cool if Customize can customize mode hooks and auto-mode-alist and other usual stuff.
It seems like most elisp packages could come with a standardized "Here's the normal setup for this mode/package; would you like to run it now, have it run on each startup, or see a new buffer where you can examine it now?", analogous to how customize-theme prompts to disallow/allow-once/allow-always code upon loading the theme. (Honestly, I assume this never happened because most emacs devs seem to prefer managing snippets of elisp over using customize.) Use-package gets part of the way there; seems like it could easily get the typical setup hooks for a package from the package itself.
~Chad