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.
If Customize can provide a interface, I’m sure packages will (slowly) adapt to it, just as they adapt to defcustom.
(Honestly, I assume this never happened because most emacs devs seem to prefer managing snippets of elisp over using customize.)
Mainly for maintenance reasons, I guess. Custom file is usually not version-controlled. That’s not necessarily a bad thing, I find Customize useful for storing local configurations that could differ between machines (executable paths, etc). Maybe Customize could separate into two files, one version controlled, one local. And I can put many of my random setq’s into Customize.