I also think MLB has by far the deepest level of talent of the three major American professional sports leagues, in large part I feel this is because of the farm system, and also of course because of its head start over basketball and football as a widely popular sport.
Who does the scouting in the NFL? Well, NFL scouts. But who do they scout? They scout, almost exclusively, college athletes.
Which means the first level of scouting has been done by college football coaches, and in general your average college football program just simply does not have the resources that a major league baseball club has in regards to going out and finding talent. I don’t care where it is in the country, what level of High School ball it is, what team it is, I’d be willing to bet money that EVERY High School baseball team that exists in the United States and has existed for more than a few years has probably had a scout see them in some capacity at some point.
And then of course you have Canada, Puerto Rico, Japan, South Korea, the Dominican Republic, Venezuela, Mexico and et cetera. In some places in the D.R., kids as young as 13 are trained every day practically all day to become ballplayers.
The farm system has its tentacles everywhere they aggressively go after talent to a degree that college football programs just can’t mimic. Furthermore, college football is more limited in how it develops players. When you are brought into the professional baseball fold, once you make it to AA ball you’re going to be playing fairly regularly with guys who have been to the show, genuine, Major Leaguers. Not the cream of the crop major leaguers, but major leaguers nonetheless.
It’d be akin to NFLers practicing and doing workouts with college teams, that level of interaction between one level of football and one level of baseball just doesn’t happen.
And since every Major League club has a AAA, AA, at least two A, and at least 2 Rookie league affiliates (and sometimes), they have a huge organization that can house TONS and TONS of prospects and give them a chance to develop. The NFL teams don’t have as much room for people to exist in a developmental capacity. Keep in mind that the Minor Leagues aren’t just feeders for the Major Leagues, Minor League baseball is financially healthy and it actually makes money (most Minor League teams are owned independently, but because they are operated as for profit businesses the farm system isn’t a total drain on the Major League club, which still has to pay all the player and manager salaries on every one of its affiliate rosters.)
In addition to the Minor League system, of course, MLB gets the benefit of the NCAA recruits as well. Many productive baseball players go straight from HS into the minors, but a good number come from college ball as well–and college has proven to be a good training ground for ballplayers. Most guys who come to MLB from college spend a very short time in the minors if they’re genuinely MLB caliber talent (sometimes not even a full season in the minors.)