Currently do to the way the games calculate turn order there are many megas that are forced to run Protect to safely mega-evolve without taking a free hit or being possibly KO'd. This is due to the game calculating turn order during the "choosing" phase and not during the "action" phase. This effects Pokémon that get needed speed boosts upon mega-evolving, Swift Swimmers, and Pranksters for example.

The question is: is this an intended feature by GF or an accident meant to be rectified in the future?