X11. It’s insecure by design, yet most distros still ship with it (understandably, since Wayland isn’t 100% yet).
This is a bit overhyped.
packaged software runs as root during the whole installation period - this means that anything slipped into the install script will have full root privileges to do anything to your system. Flatpak does fix this, but normally-packaged software is still abundant.
WTF? Things that run as root, do. Things that don’t, don’t. Obviously most things don’t.
any non-root program can change aliases in your bashrc or bash_aliases file. I.e. they can change “apt install” to some other nefarious command, or to point to a dodgy software repository, so that next time the user types “sudo apt install [XYZ]”, it downloads malware or does other nasty things.
For your own user, so what?
EDIT:
But it’s not an insurmountable problem, IMO. Distros and DEs will just take time to adapt.
Actually it is. One can make levels over levels of isolation, sandboxes and more sandboxes, but in the end conscious hygiene matters most.