Looking at the likely rosters for next year's farm teams, I think the talent is close to being restored. Here's my analysis:
You'll have Castro (top 100 prospect), Chris Johnson (thinking Houston will go with the Blum/FA/Keppinger platoon again), Bogusevic, DeLome, Vallejo, Van Ostrand, Locke, and Sutil. All of these players still project as major league contributors.
In the rotation, you'll have Trinidad, Wright -or- Paulino, Wilton Lopez -or- Yorman Bazardo, and Sergio Perez. Again, all of those players are still prospect-age and project as future MLB contributors. The bullpen will feature guys like Lo, Meszaros, and Englebrook, all of whom faired really well in the AFL. When you factor in that the Houston roster will have prospect-age players like Norris, Gervacio, and Arias, the later-level farm is set IMO.
In AA you've got guys coming off of MONSTER years (Clemens, Gaston, Shuck) as well as former high draft picks (Einertson, Flores), so the outfield should be stacked. I'll concede that the infield will be mediocre, with low-ceiling guys like Meyer, Cabral, Simunic, and Suarez.
The AA rotation will be top notch, with at least one of the Lexington studs in place. I see a starting 5 of Lyles, Arguello, Abad, Cespedes, and Hudspeth. Lyles, Arguello, and Abad have all had really good numbers so far. The bullpen may not have any top 100 guys, but will be filled with players who are still very young (Urckfitz, Tilghman, Hallberg, Mowdy, Powell).
The lower levels will feature many highly drafted guys (Austin, Steele, Mier, Wikoff, Meyer, Hernandez). I think Mier, Austin, and Steele are all future top 100 prospects. Under the radar prospects like JD Martinez, Ebert Rosario, Jose Altuve, and Eric Castro add depth.
The 4some of Seaton, Bono, Greenwalt, and Dydalewics make for a solid high A rotation (unless one or more ends up in Corpus). High ceiling guys like David Duncan, Dallas Keuchel, and Brandt Walker add depth, and that's without mention several younger players who have shown potential (Colton Pitkin, Luis Cruz, etc).
Overall, I think with 1 or 2 more good drafts, the HOuston farm will be top notch. Heck, in 2 years, we could have up to 7 MLB-ready outfielders with nowhere to play because of Bourn and Pence. I just hate seeing "shambles" continually associated with the farm because while that was true 3 years ago, I don't think it holds today.