For me, it's less of a macOS inherent issue and more so that many, many things just assume Linux by default. Anything you find on GitHub that relies on some sort of native module is really hit or miss in terms of "will this just work, or will I need to go waste a couple of hours or resort to a VM?"

For example, I've run into a couple of occasions where I've needed to build some third-party thing that happens to also need something like QEMU, but the build scripts only run on Linux. Annoying, but whatever, setup a Linux VM/"container" and good to go, right? ... except there is no nested virtualization support on the M1 macs.

Outside of those sort of issues and other ARM-specific problems, while it doesn't usually impact my workflow too much, I wish I had more control over the system. I wish, for example, it could boot off of something other than APFS, etc. I don't want to have to deal with Time Machine when I've already got snapshots everywhere else, etc.

Everything is relatively minor, but there is always some new thing that makes me annoyed every week or two.