I think another thing that is hard to quantify in this advanced stat era is the chemistry of the clubhouse, that leads to attitude (I will pick you up), that leads to clutchness, that leads to team success, that leads to chemistry, that leads to attitude...you get it.
Philly decided to build on advanced stats (from the management down to the individual players). There are many reasons why several key free agents picked to play somewhere else and they ended up signing players just like tier MO.
Good players but "ME first players" across the board. Think of the key offensive players on their team. (Harper, Realmuto, Herrera, Mccutch (to a lesser degree)) have never been know as team first players. The results, better statistical players than last but the same results.
Compare to who AA signed this year. What is Snitker known for (clubhouse)? What is the constant talk about team (Acuna, Albies, Carmargo, Swanson)? What is Freeman's main attitude about resigning? What are McCain & Markakis known for (except being old and past their prime)?