I get your frustration with people painting with a broad brush around intelligence and baseball. Obviously, this notion doesn't apply across the board, as evidenced by some of your former team mates and yourself. I would, however, point out that there is such a thing as baseball IQ, and that doesn't necessarily translate to traditional IQ. A couple of examples, just off the top of my head are Johnny Damon and Chipper Jones, two guys that could definitely play, and were baseball smart, but lets face it, they aren't going to win any academic bowls. Chipper is on Atlanta radio a lot, and when it comes to baseball, he's got great insight, beyond baseball, oh boy.
The bigger reason to me though, as to why baseball is being considered in this light is this explosion of the travel baseball, it's culture, and the notorious baseball dad. What you are winding up with, is 11 year olds playing a major league schedule and being in an echo chamber where baseball becomes everything. This isn't healthy, and I've got news for all the baseball dads out there, it's not helping your kids chances. At a certain point, it comes down to the fact that either you have talent or don't, and while some display promise at these younger ages, the amount of energy solely devoted to this pursuit at that age is ridiculous. What has developed around the sport is a culture that foregoes almost everything else (including balanced focus on academics) in favor of baseball, and this isn't healthy at all. Basically, you've got hundreds of thousands of Marv Marinovich's out there psychotically pushing their kids, it's not gonna turn out well for them.
I don't have a son, but if I did, I would not at all allow him to be in this sort of environment. It's important for people to have exposure to lots of different sports, activities, and pursuits (to include academics), especially at a young age. Perhaps parsing things down at an older age, say 16 or so makes sense, but the current psychotic nature of what is going on in youth sports in general is out of fuck control.