While I generally agree with the theme here, I think it's important to note that fans often pump prospects up higher than their ranking or value around baseball for various reasons. Some thought Henry Owens was a future ace, or #2 but he never had that potential pedigree as a prospect. WMB was highly regarded because he was our #1 prospect, but he was also a #1 in a system that was regarded as weak at the time and wasn't a top 50 guy like Bogaerts, Swihart, JBJ, Betts (was slated to be #9 before he graduated). Sure, there are also your Kalishs, and Websters, and Hansens, then there are other guys who developed elsewhere such as Reddick and Lowrie. Sometimes guys get hurt, I'll always wonder what could have been with Ryan Westmoreland.
Still, if you look at the WAR of our top 100 prospects vs. the WAR of all other teams top 100 prospects over the last 10 years I think we've done as good as if not significantly better than any other team. Our guys pan out better, so I think we should put more stock into our own prospects.