This here is the problem with linux on the desktop.  You have programmers like Slated here thinking inside a very narrow definition.  He wants X11, now Xorg, to be modular at the cost of convenience.  He's willing to put up with inadequacies like this just so it remains in his narrow definition of what it should do.  And your trying to connect the clipboard with security doesn't jive.  Linux I find on the servers I run gets updated just as often as windows does.

I find the copy on select and middle click paste functionality abhorring.  It is so error prone that only those who specifically know what they are doing, programmers and advanced linux users, can use it.  And the only reason why it was implemented the way it was, was because they didn't want to change the terminal commands ctrl+c and they wanted it to work in a terminal first and that should be how it should work elsewhere.  And the people who could implement it refuse to because they don't like it.  They instead in their arrogant way, assume programmers who are use to the method that windows and mac os x do to work with the clipboard, think they will change their ways just to create their app on linux.  Seeing the number of applications that don't comply with this goes to show that those programmers of windows and mac os x refuse to give in.  That they want the clipboard to be just like it is on windows and mac os x.  Telling them they need to add low level access just to deal with the clipboard on linux is stupid.  All they should need to worry about is copying the data to the clipboard.  The clipboard should worry about keeping this data.  Not the app that the data was copied from.

And besides, X11 and Xorg is ancient.  It was dropped by google on android.  Ubuntu and Fedora are moving away from it to wayland.  it's just a mess of patches of kludge fixes that it's beyond saving.  You can't implement anything modern on it cleanly without it ending up being a kludge.  No one really uses the remote network capabilities of it anymore.  It being modular has actually hurt it.  And besides, it's not the 1980's anymore.  We got computers that are way more powerful then that with a lot more memory that can easily deal with a persistent clipboard.  So it's time to get away from that.  It's what end users are use to.  Don't be afraid to use the resources you are given.

And the temporary solution of running a program to fix the clipboard is a problem in itself.  You need to install it and most of the time they only support text.  What about video, audio and other types of binary data?  This was known about in 1993 and in a couple years it will be 20 years since the problem was known about.  To say open source moves rapidly isn't always true when it comes to features end users want and programmers don't care to implement because no one is paying them money to implement it.

Ubuntu has done a good job of making things easier but these fundamental features need to be their.  That's how you'll become mainstream.  I kept hearing every year from 2000-2010 that this year was gonna be the year of linux on the desktop.  Well it hasn't happened.  And the typical back pedal response was that we don't want to become mainstream then.  So instead of fixing the problem, we'll just come up with another excuse not to fix it.  Great job guys.