I think part of the problem people are having with seeing the upside of this rebuild is that, for years, the Drayton-led FO was feeding us lines of bull about guys that were "top prospects". Guys with huge holes in their game like TJ Steele, Colin DeLome, and Jon Gaston were in the top 5-10 who wouldn't even sniff the top 40 if they were in the system now. Our #1 prospects from 2004-2006 are all out of baseball already. 2008's (Towles, whose ranking was based on one stinking game, however great that game was) probably will be soon. 2010's #8-10, all out of organized ball already. Looking back, these guys were like the best dressed at a 70's prom. Even then if you had any sense you knew it was gimmicky.
In 2011, with the Astros finishing 56-106, the Astros had the 26th ranked farm system. They were bad at every. single. level. Because of Drayton, and Tal, and Tim Purpura. That's what trying to patch the major league roster will do to an organization over time, unless you can support a $200M+ payroll, which the Astros can't. Now, they're on pace for about the same record, but by many accounts have a top 5 system. Some have even said the best in baseball. That's progress, no matter how you try to spin it. Let's look at what having the top farm system has meant for other teams in the past, looking at their major league record that year and what it meant for the club going forward:
2003: Cleveland Indians, 68-94, 93 wins 2005, Playoffs 2007
2004: Milwaukee Brewers, 67-94, Playoffs 2008
2005: Los Angeles Angels, 95-67, Playoffs 2007, 2008, 2009
2006: Arizona Diamondback, 76-86, Playoffs 2007
2007: Tampa Bay Devil Rays, 66-96, Playoffs 2008, 2010, 2011
2008: Tampa Bay Rays, see above. See how perennially ranked farm systems can sustain success?
2009: Texas Rangers, 87-75, Playoffs 2010, 2011, 2012
2010: Tampa Bay Rays, do I really need to make this point much more?
2011: Kansas City Royals, 71-91, currently at .500 for 2013 (ok, they're not helping my point here)
2012: Texas Rangers, yep...again.
So many well-respected people who make a living off of knowing these things continue to praise the talent Luhnow the Astros are now collecting in the minors. He has the track record, whether you want to believe it or not. From Grantland: "According to Baseball America, more players on Opening Day rosters this year were signed by Luhnow than by any other scouting director."
The word from those who see the inside of the clubhouse is that Porter is doing a good job keeping these kids invested in the team, despite the constant flow of losses. Outside of Harrell, the attitudes of these players is largely positive and they're building a team atmosphere.
I know it's hard to look a little deeper than the current stats and standings, but have patience. The milk was spilled several years ago. It's time to quit crying about it and accept that it's time to clean it up.