They make it much harder for an independent team to make the playoffs. You are actually now more incentivized to join a conference. Because at least the top five or whatever conference champs get in. There is no way with these large conferences with so many good teams that they are going to give up those free spots to an independent.
So yeah, I guess if you love independence, this could be a bad thing. And definitely if the door is shut on the AAC because that’s your best option.