I feel like something will have to change soon though, because so many younger audiences are exclusively watching online and on their phones/not being counted by Neilson, and that number is only going to grow.

Exactly. Many people aren't watching live television anymore because there are other alternatives to watching something, so traditional media relying on an ancient (often unreliable) system to count numbers isn't going to help matters in the long run. They are only hurting themselves if they aren't going to adapt and keep up with the times, which then fucks everyone else over in the process. It's a lose-lose situation, basically.