Klentak's flaws were obvious but he also never really had the opportunity to run the team for real. MacPhail (without whom he obviously never get the job) was too weak a leader to back him properly, and the old-guard people still held him back (plus he either made a huge mistake - or didn't have a choice - in keeping so much of the old regime and moving so slowly to change that).
Middleton has also gotten better, but more importantly, hired someone he trusts more, and who can stand up to him. I would argue Middleton's Girardi hire was worse than the Kapler hire (in part because the GM wasn't empowered at that point either). And that Almaraz turned out to be a worse hire than Klentak. By the time Klentak actually hired his own development team it was almost too late (and he didn't really hire Barber either). I seriously doubt Klentak was so dumb that he couldn't see the organization needed to be aligned from the minors to scouting to the majors - he just didn't have the clout or management skills to get that. Remember, when he was fired the leaks were that he'd alienated a lot of longtime org people. But I don't know that those people have any power now either.
What's ironic is that Sam Fuld was a big part of the original failed analytics braintrust, and now he's crucial. I think DD has exceeded nearly everyone's expectations in terms of not just being a win-now, major league-only focused President, and creating a diverse (intellectually and otherwise) front office.
In the end it's the same as the Wade narrative. All GMs are doing to do some good things, by luck or design, many of which will linger past their tenure.