Ugh. The Achilles heal of the Linux desktop experience (or "one of", is probably more accurate) rears its head.Then the question arise: How many percent of Linux users do know about he middle mouse (or wheel) button "paste any previously highlighted text" ?
This is my most often workaround for the terminal issue. Otherwise just use Shift+Ctrl+C and likewise when paste.
Modern Linux desktop apps have been moving towards a more Windows-like copy/paste model, where merely selecting text in newer apps does not, in fact, copy it to the clipboard. It's app-specific, so you have to know how a given app behaves.
As for middle-click-to-paste, that's the reason my last pointing device (a trackball, actually) wore out - the click/wheel's switch failed. I'm guessing they didn't expect nearly such heavy usage and probably used a cheaper switch than the L/R buttons.
BTW, my terminal emulator of choice is still good, old xterm. It's fast, light-weight, configurable enough, ubiquitous, and has all the original X11 copy/paste semantics. I don't need tabs or any other features of newer terminal emulators. Also, their window decorations tend to consume too much screen realestate for my taste/needs.