Proper macOS virtualization, for example.
Also, I do not want to have to upgrade my machine and OS every few years just to keep up with apps that stop working or installing, not because the hardware is no longer capable, but due to ridiculous obsolescence policies. Heck, I can not run the latest version of a lot of software (including basic developer tools) on one of my MacBooks, simply because it is running Monterey.
A proper package manager CLI is also sorely needed. Delegating that to Homebrew and MacPorts doesn't cut it.
Even my MacBook Intel from 2015 is still receiving updates. It's slow, but everything works.
Honestly, Homebrew is so healthy[1], and modern Apple is so corrupted by greed, that I'm sure I don't want Apple to try to Sherlock it. Can you imagine? To get a package published, you'd need the developer subscription, and Apple would block any package that threatened any of their revenue streams. Not to mention that they'd probably want to also run the scan the MAS does to ensure you're not using any "private APIs." No thanks, Apple has no role to play here.
[1] (Personally, macports hasn't been my jam in decades)