Personally I find it amusing this "feature" has survived all this time, all the way into modern linux desktops.
Inertia is a powerful beast indeed.
I understand the reluctance to throw out such decisions, even if they were made over 20(!) years ago, because inevitably the vocal minority will jump out of the woodwork and declare how they can not possibly live on without this feature.
However at some point common sense has to take precedence in UI design. Otherwise you end up with a trainwr^W^Wthe linux desktop.
No UI design perfectly suits every human; every UI design requires some level of adaptation to use efficiently. UIs that optimise for discoverability already exist; Windows and Mac OS X both do fairly well. The traditional Unix desktop has a different focus - why must people who use the traditional Unix desktop and are happy with it be forced to adapt to something else? Why can't we all just get along?
Put another way, the iOS interface, by rapidity of adoption alone, would seem to be far superior to traditional desktop-paradigm UIs. Would you agree that "common sense has to take precedence" and Windows and Mac users should have to abandon their systems and use iPads instead?
No, but having used the linux desktop for over a decade (last stop was the ion3 wm) and now OSX, I have come to the conclusion that some of the wrongs with X11 just have no excuses anymore.
While there may still be (weak) arguments for preferring "select-to-copy" over "CTRL-C-to-copy" there is not a single argument for maintaining the mess of multiple inconsistent copy/paste methods in parallel.
This is not a matter of polish, preference or imitating what others do. It's a matter of finally applying the no-brainer lowest baseline of common sense.