Well pitches are being called from somewhere else other than the catcher now. That certainly is a good example. Also, just the fact that they dont allow starting pitchers to stay in the game. Baseball been around for more than 100 years, you think its some great new revelation that no one considered that pitchers dont do well after going through the lineup 3 times? Of course they considered it, but still left them in there anyways because it teaches the pitcher to pitch when he doesnt have his best stuff and to save the bullpen. The mentality is much more about the pitcher being a disposable machine to be used up and replaced. Pay them and use them just enough to keep them, but not enough to give them any power themselves.
BTW, I'm not saying theres nothing good in analytics, on the contrary, its evolved the game and won some championships, including '04, I'm just saying they've gone too far. There should be rules in how theyre used, like no in-game advice giving. No pitch calling.