I personally think the follow me feature is one of the most overrated things in the history of the Pokémon franchise... But! If done right, I'm fine with it.
By done right, I mean YOU choose the Pokémon that follows you, and it can be ANYONE of the six you're currently carrying, not the first. Because, if you're having a mon follow you, it's because it's your favorite one. So, even if fainted, the mon I choose should be the one that follows me, and not necessarily the first one in the party.
I mean, in Yellow, Pikachu followed you regardless of position in the party, I'm sure they could do something similar in future games, too. You assign a Pokémon the role of "follower", and it follows you whenever it's in the party, and even if fainted.