> Decent package manager, brew is awful compared to apt.
Use Macports. Installs itself properly out of the way in /opt. Works with the Apple frameworks (eg Python), allows multiple versions of software to be installed in parallel (using port select).
> Window snapping can only be done on Apple keyboards not on external keyboards.
Yes, you need some free 3rd party apps for affordances that should be built in. Hardly a deal breaker.
Rectangle allows you to set the hotkeys for window snapping and sizing for example.
As for scroll directions, yes, it's different to Windows, but it's the same on the Mac and iPhone. Didn't take very long to adjust.
Agreed that the new Settings app is a PITA and obviously inherited from iOS and sucks, but how often are you accessing Settings?