Milotic is too popular to not get a mega evolution and it's the most beautiful Pokemon. If Mega Milotic did not exist, Game Freak would say they couldn't come up with a decent design in that Flygon interview.

I think there saving Mega Milotic for Wallace in a Hoenn/Kalos crossover called Delta Z or Delta XY. All the references to Match Call, Champion Wallace, and the Battle Frontier are alluding to something... Lets not forget the reference to a high speed ship being built with rail technology from Kalos.