I agree with comment #13 - middle clicking on a mouse's scroll wheel is quite difficult and clicking left+right buttons together is easier. Some mice are worse than others for this (some have too little wheel resistance), but all of them require more care to click on the wheel (without scrolling it) than clicking buttons.
So among other things, this is an accessibility issue.
Also as I mainly use a laptop, I'm used to clicking the two touchpad buttons for pasting text, so it feels more natural to do that with a separate mouse, on the rare occasions when I use one. But that is of course quite personal.
I understand the rationale for upstream's change, but I've never noticed noticed the single button lag or any problems arising from it. But maybe I'm just used to it.
Finally, the obvious thing that seems to be missing is a tick box under System -> Preferences -> Mouse to decide this behaviour. Editing xorg.conf for something like this makes no sense when other basic mouse preferences are configured via the GUI.
The idea that only power users use middle-click to paste and power users can edit xorg.conf (comment #4) is nonsense (as well as being an example of a logical fallacy). Lots of GUI text-pasting users never edit system files or do any system administration at all, and even some casual users learn that way of pasting. Even if that's minority usage, they aren't the same subset as those who are comfortable using sudo and editing config files - or even using the command line.