The Phillies fundamental woes are being a young team that's not ready to compete, all three young starters have essentially melted down the last month (stress, arm fatigue, mental fatigue), even though the bullpen has righted itself and is now one of the deepest units in the ML.
Hernandez is coming around, I think it's obvious the foot injury really hurt, Herrera is a flake, Rhys is finally back on track.
Kingery, Crawford weren't ready for prime time, Quinn can't stay healthy, Alfaro is a work in progress, Franco got hurt, this team would be in a deeper hole without Cabrera and Ramos.
The only serious asset lost in all of Klentak's moves was Kilome, who was marginal for the 40 man roster, and letting some guys leave as DFAs in August rather than as claims in November (Thomson, Lively, Leiter - none would have been kept on the 40 man roster this fall).
I thought this team was a .500 team at best in the spring, 75 wins before they added Santana and Arrieta, so no real surprises, Franco played better than expected, Hernandez and Herrera worse, Williams better, Altherr much worse, Crawford and Kingery worse but both were question marks this year in any case.
What will solve the defense are young players with defensive skills hitting, if Crawford posts a .270./.350/.400/.750 slash line Cabrera isn't obtained, if Quinn stays healthy we have a top CF, if Altherr and Herrera hit corner OF is set, and so on. I don't think launch angle is the issue with young players struggling, rather a combination of factors with a new coaching philosophy, some which will just need adjustment time, some which will need changes in player personnel.
Rebuilds take time, how much time is a matter of scouting, coaching and luck - if a couple players emerge faster than expected it takes less time, if a few top prospects flame out it takes longer.