I've always felt that the typical way to compile organizational farm rankings wasn't good enough. Judging any one prospect is tough enough using all of the available data, if you can get it all.
That said, we have trades, and the order in which players were drafted, as hard evidence of teams' opinions to anchor around.
Judging an entire farm system is much tougher. There is no hard data about the opinions that teams have about the strength of a system as a whole. And subjectively deciding that this group of 30 players is better than that group of 24 players is invariably full of bias; our brains can't consider all 54 players independently from those two teams, much less 30 teams' worth of prospects.
When I worked with an MLB club, then later at FanGraphs, and now at ESPN, I've used the Future Value system. It's scaled to WAR (an all-inclusive number of how good any player is, measured in wins) and adjusts for proximity to the majors and risk. On the team-by-team top 10s, I spelled out the FV grades for more than 300 players, listed about a dozen more prospects for each team, and I had about another dozen or so for each team whom I could have listed: the average number of players on my list for each team was 39. (For those wondering, I have updated the FV grades for recent Tommy John surgery announcements on Tigers LHP Joey Wentz, Padres RHP Reggie Lawson and Padres RHP Andres Munoz.)
The next step was something Craig Edwards did for us at FanGraphs last year, using the last couple of decades of players to figure out how much a prospect is really worth. The idea is to take every prospect and put them into a bin based on how they were ranked as a prospect, then look at what their career was like, then do some economic adjustments and assign values to each bin, which are then applied to every prospect. The output is a number that represents what a team would bid for each prospect if he was at auction and the team was trying to value its six to seven controlled years in the big leagues before the player hit free agency. The top prospect in baseball, Rays shortstop Wander Franco, is worth $112 million, which means we expect he'll produce $112 million of value above his salary for those six-plus seasons before he hits free agency; he might make $50 million in salary during that time.
The cutoff for what players make the list is still somewhat subjective. The concept is any player with real trade value: When you see a guy traded who isn't good enough to be on here, it's usually as a placeholder in a salary dump trade, whether it's a late-round pick in the low minors, a back-half-of-the-roster type in the middle minors or an upper-minors player who is likely to be on waivers in the next 12 months. Sometimes a player emerges late and I haven't updated his rating, most commonly at the lowest levels of the minors at the trade deadline, but updated scouting reports usually come to the surface the day of a trade.
Reducing complicated, unique people into numbers, and more specifically money, isn't a great feeling, but it's not done to change anybody's career, merely to measure which team is doing the best job at cultivating young talent. There are some instances where two teams are within a couple of million dollars of each other, and in those cases the advantage is given to the team that reached that value with the fewest amount of players. I've also made slight adjustments where teams benefited from having bulk value of prospects that, on average, aren't list quality. The Mariners (one spot), Giants (one spot) and Blue Jays (two spots) were the teams whose rankings were impacted in this regard. Functionally, think of the average value per player as the tiebreaker when two teams are close.
For this reason, I encourage you to look at the rankings in tiers; if one midlevel pitcher goes down with surgery and his grade is downgraded a notch or two, some systems could move down three or four slots. In total, there are 1,182 prospects and $6.53 billion of surplus value in the minor leagues by my system. A more complete picture of the young talent within an organization would include big league talent (most recently suggested by ESPN's Karl Ravech) -- that's on the coronavirus shutdown to-do list.