X's copy/paste behavior was meant to be used in conjunction with the secondary selection which is seldom used these days as most modern toolkits don't expose support for it.

Linux needs a preference layer between keyboard and app.

This already exists in desktop environments. Of course, not all desktop environments have the same features. I know KDE Plasma has this. It can't work with all apps though, for the same reasons that MacOS and Windows can't have a feature like this that works with all apps. That is, unless you want to translate keystrokes into other keystrokes on a per app basis.

What's a "middle click"?

A way to insert X11's "clipboard" buffer (i.e text that is currently selected text).

I agree with GP: I find the two separate copy-paste methods very useful and wouldn't want to see them merged. Users who aren't aware of one of the aren't affected, and those who are get an extra buffer to use.

Clicking with the middle mouse button - nowadays, it's typically a clickable scroll-wheel, but it used to be a plain button between left and right mouse buttons back in the day.

After mice had mostly standardized on two buttons but scroll wheels didn't exist yet, it was common to map a simultaneous click of both mouse buttons to simulate a middle click.

Assumes a three-button mouse:

http://ecx.images-amazon.com/images/I/513VKV7DZBL.gif

Usually a scroll wheel, now.