PG - great post!
Some off the cuff stuff here since it is cold outside and waiting for the SB!
I do believe there are fair opportunities in the minor leagues for non-bonus guys. bbscout used to say that if you hit .300 every year and at each level that you will eventually find yourself in the big leagues. That may be true, but I agree that there is luck involved as well. Billy McMillan was a great college player at Clemson and a career .300 hitter in the minors yet his big league career never quite took off. Obviously it is a huge honor to even make it to the majors but I wonder with him if the stars never quite aligned. More than just having a plus tool like hitting however, sometimes they are looking for more. Outfielders without blazing speed, maybe more power is exepected nowadays. In every case, especially with top draft picks, clubs are looking for dominating players not just guys who are adequate.
Some organizations are valuing players differently these days with modern statistics playing a role. Boston and Oakland are two that come to mind. Beyond homeruns and rbi's, for example, are categories like on base percentage, weighted on base average, and even quality at bats. At the end of the day, the idea is to win. Other organizations just seem to know how to draft. Minnesota is one that comes to mind that consistently produces. The Yankees also seem to be very good at picking talent imho. I am sure I have missed some but those come to mind. There is obviously luck involved in picking the right players and luck that they ultimately develop.