I think the issue is that entering Year Four, Middleton got impatient. Last year's team was supposed to take a run at the wild card with a second-year manager, this year's team would have built on that by winning or at least coming close to winning the NL East (while also making the playoffs). Then you'd shed Arrieta and Santana's $ and reload. Spending $200 million was certainly not part of the plan.
Not saying that plan was actually going to work, clearly they made the moves they did because the cheap/internal options had failed. And I certainly won't argue that it was Middleton, rather than Klentak and his team, who decided Williams, Crawford and Alfaro were not going to be part of a winning roster, though I think his decision to replace all three of those players was due to Middleton's impatience.
Changing the 2019 expectations changed everything. People (including the handicappers) expected 89-90 wins and a possible division title (presumably with an NLCS loss at best) instead of a maybe-wild card, and when it didn't happen the manager didn't even get a third season. And Klentak's patience with the guys he did keep (VV, Pivetta, Eflin, Franco, Hernandez, Herrera) also came back to bite him.
The Original Sin is still what happened before Klentak was hired, but he and MacPhail's decision to slow play everything is the other. They wasted two years with Mackanin. 2016, especially, was sold as a year that didn't even count, just for evaluation. All 8 starters from 2017 are out of the organization. Only 2 remain from 2018. And the revamp at the top of the minor league and development/scouting levels was still puttering along over the past two seasons, while the 2016-2017 drafts may fail to produce a plus everyday player (we'll see). So it's hard to see what's failing now as the culmination of any plan. They've just been winging it, and to add insult to injury the only two good inherited position players who you were supposed to be able to write down in ink are floundering, while a third self-destructed.
Anyway, we look like sellers, huh?