I don't remember who made the comment to me on Showdown about Megas, but Kurotsune's response was this.
[10/10/15, 4:19:52 PM] Kurotsune: Well, pairs are randomly assigned
[10/10/15, 4:20:14 PM] Kurotsune: So feel free to use a mega-evolution knowing full well that if your pair also has one, that's one pokémon that runs the risk of becoming useless