Okay, this was indeed an intentional upstream change in xf86-input-evdev. The changelog happens to carry some reasoning, too:
Author: Peter Hutterer <email address hidden>
Date: Fri May 28 09:47:17 2010 +1000
Disable middle mouse button emulation by default.
The AUTO feature was the default, MB emulation was on until a middle mouse
button was pressed. MB emulation however results in a delay of the first
press, causing minor annoyances to the users and being generally confusing
when the behaviour before a button press is different to after a button
Disable the feature by default instead. There's not a lot of two-button mice
around anymore though and the inability to detect two-button mice makes for
non-deterministic detection of when the emulation should be on.
Middle button emulation can be enabled with a configuration snippet:
Identifier "middle button emulation"
Option "Emulate3Buttons" "on"
So, this is a little different than I thought. (And it even teaches me something I didn't know: it's hard to detect if a mouse only has two buttons!). We should keep an eye on what other distros do with this change. If Fedora, Debian, etc. choose to revert it, we should probably consider doing the same. Otherwise, it's effectively the new standard.
Another thing to keep in mind is two-button mouses / middle clicking in general / left+right to middle click are kind of power-user features, so we can expect power-users to be happy configuring these things.
I think this should definitely go in the release notes :)