This isn't true. The prospects that you think were part of a supposed "second" farm system infusion were actually in fact a part of the one and only major prospect haul...they were just in the low minors when the Marlins/Dickey trades were made. Even Anthony Alford was already drafted prior to those trades.
There was one big prospect haul, back when the draft and IFA system were exploitable. After that window closed, our prospect development took a significant tumble.
You're allowed to like him as much as you want, but this is a stretch as well. He was clearly learning on the fly and had to endure several mistakes, which means that he wasn't "always" the GM that you believe him to be. Some of his pitfalls throughout his tenure included: undervaluing defense, undervaluing character, and overacquisition of old players on over expensive contracts: deals that handcuffed himself from a payroll standpoint, and deals that he ultimately had to juggle his way around.