I have always favored Pidgin over Empathy. I think Pidgin is more feature-rich client than Empathy. Still didn't get a good reason Ubuntu replacing Pidgin for Empathy as default IM client.
I assumed the change was that Empathy was developed specifically by the Gnome group, and included as part of the official Gnome releases. Previously to that, Pidgin was considered by Gnome to be the preferred client, and Canonical was just following Gnome in switching to Empathy.
I was the gaim/pidgin lead dev. for many years. That's pretty much the gist of it, from what I can recall. While we aimed to be more cross platform, empathy was more focused on straight up gnome integration.