The original sin of the rebuild is still the failure of the Amaro era. It's pretty shocking (and in some cases, unlucky) that not one of Altherr, Williams, Herrera, Quinn and even Randolph could hold down a starting OF job. And I'm sure in 2015 we thought our Franco/Crawford/Kingery/Hoskins/Alfaro IF looked pretty sweet. Starting pitching also looked deep, if lacking any future ace (but Nola wasn't supposed to be that either). Even if only half that core had panned out it was going to be easy to fill around it.
Of course, the failure to have any help now from the 2016 draft is also a problem.
But the team's not a disaster. These are all fillable holes.
Segura seems to get traded every two years, so who knows. He probably stays for the same reason Franco and Hernandez did the last two years - value on the roster is still greater than the trade value. I think Segura can bounce back - he was also hurt a couple of times last year - but I would certainly trade him for peanuts if you can use the money to sign both Gregorius and a 3B and be free of the obligations going forward.
I also don't think Santana's struggles were the Phillies' fault. He might have done very well this year after one season of adjustment, but Cleveland and the AL was clearly more comfortable for him. He also wasn't that bad, just not amazing. His lesser defense was the real surprise and maybe that was on the coaching staff (as so much seemed to be that season).