I agree with the point about this being configurable.

About your first point, however, keep in mind that "middle click insert" has been the default behavior in X since the 1980s, long before Windows or current generation MacOS's were around. To me, this is such a basic functionality, I would compare it something as fundamental as CTRL-X/C/V for cut/copy/paste on Windows.

That is gnome's standard play: move a feature to a preference (“you can just turn it back on”), remove the preference from the control panel (“you can still turn it back on using ‹whatever conf backend they're using this year›”), and then finally remove the feature (“you could only turn it on by using an unsupported mechanism, and ‹conf backend they used last year› is deprecated anyway”).