An average farm system should have some crappy players, some mediocrity, and some potential stars. Ours seems lacking in the latter category. A farm system with just mediocrity seems below average to me.
Most of the players you mentioned played in AAA ball. Wade's wave of draftees or the bulk thereof just started getting to AA last year. Lyles, Martinez, and Castro were fast tracked and thus the exception not the rule. BTW I read one web article that said that the Astros farm system ranked 15th going into this year. IIRC the farm was ranked about 22nd last year. I am unsure about how to rank the Astros farm system. Lyles, Martinez, Altuve, Paredes and Castro arguably on a more successful team would be starting the season in AAA. That would raise the farm ranking. On a more successful team, the stars would not be traded, so the farm would not have some of its current top prospects like Cosart, Singleton, Jonathan Villar, Clemens and Santana. Without those trades, the farm ranking would be lower. Only after the Astros stop fast tracking prospects and the farm stabilizes will we know the real quality of the farm system.