This usually happens when you do non-standard things like try to change the desktop environment and then update to a new major version. If you pick a distro that is already close to what you need in the first place, this should not be as much of an issue.

Source: Personally got it into a state where it became a huge headache to update.

Ditto for windows.

Source: Personally (like the other poster) I have got both into a state where it became a huge headache to update.