Look, I get it. Prospect rankings are iffy. There are too many external factors, too many variables. Maybe your top prospect is going to lose out on 240 plate appearances because he got caught smoking pot. Each talent evaluator goes by what they see, and of course have their own system for ranking. Throw in the possibility that you don't even like the talent evaluator in the first place (see: Law, Keith), and you're going to have a very loose set of rules for something that hardcore fans take very seriously. As KevinBassStache reminds us, Jim Callis of Baseball America put the Astros system at #10, John Sickels of MinorLeagueBall at #11. Keith Law had them in the Top 5.
But at the very least, the rankings can provide an overall sense of the system's health. By Keith Law's rankings, the Astros went from dead last in 2009, to 28th, to 27th in 2011 and 2012, and now he has them at #4.
How does this compare to the Astros' new competition? It puts the Astros as the top-ranked farm system in the AL West (again, going solely by Law's rankings). The Mariners (#8) and Rangers (#9) are in the Top 10. Meanwhile, the A's (#22) and Angels (#30) apparently have pretty terrible systems.
Of the Top 15 farm systems in baseball, eight of them are American League teams. The AL East and AL West have three teams in the top 15, and the AL Central has two.
I don't know enough about other teams' systems to know if the talent which is being so highly regarded is in the higher reaches of the respective system, or lower. Regardless, going from 30th in 2009 to 4th in 2012 is a good sign, and provides a little respite in this, our winter of franchise discontent.