I think good organizations can always weather a few bad people, whereas bad organizations only succeed in fits and starts when they manage to have a few good people.
The combination of Arbuckle and extremely favorable draft position was clearly the key to the success of that era in spite of ownership and culture being basically the same; Wade's role was mostly to do no harm (and be so patient/unable to get over the hump that he got himself fired). Gillick and Amaro were obviously very successful GMs at the major league level (and many if not all of Amaro's worst moves were also driven by Monty and Middleton) but that era wound up being a disastrous combination of bad drafting/development along with picking high, losing comp picks, and short-term trades.
Also you can't paper over the fact that Wade's two biggest moves were losing Schilling and Rolen. We just know that's on ownership too (much as Drew was).
Clearly nobody since then - Wolever/Almaraz, Chuck Lamar/Jordan/Bonifay, Klentak - did much of anything right.
It remains to be seen if Dombrowski or anyone he's hired or plans to hire are among the people who can transcend the organizational culture. It certainly doesn't appear so, given the continued philosophical/personnel churn/whiplash, the way they seem to tacking back to old-school approaches, and even the fact that the one younger person in charge was part of the failed analytics era.
The underrated/unaddressed flaws, as many have noted here before, might be international. But also pro scouting (the guys who picked all the prospects we acquired from 2012 to 2015, or even before that, i.e. the Lee trade). But that's also one of those hard-to-parse scouting vs. development issues.