This is not really looking at the same farm system. First, we don't really have lots of 5;10", 160 pound shortstops. Just about everyone is bigger these days. Yes we are teaching a certain analytical swing to add more power, but that is because power is more valuable. We don't really have these legions of selective hitters that we are teaching to be less selective. Often a hitter in the lower minors is drawing walks because of pitchers that can't throw strikes. Their walks decline in upper levels because the pitchers are better. And they need some power to increase their walks against better hitters. That will be a key Crawford element as he will not draw many walks without a bit more power.
Nobody really talks expanding the zone as well. They are talking about getting a good pitch to hit. And also putting a good swing on that pitch which requires an aggressive approach. Try waiting on a 98 mph fastball to see if it is a strike. Only the best hitters can do that. Most hitters pick their spots in the count to get a good swing in. That is what Bryce Harper does all the time. You try to identify the pitch and a zone. If you think fastball inside then you can put on a swing that can do damage to that fastball even if it is a little off the plate. With two strikes one should change their approach and protect the plate even if it means swinging at balls off the plate a bit.
We just are not teaching the same way as we did 20 and 40 years ago. Some things of course are similar. Hitting is always a mix of patience and aggression. And it's harder now with everyone throwing 98 instead of 88.
The philosophy is less the issue than the scouting and drafting. Johnny Almaraz was pretty much a disaster (Randolph,, Moniak, Haseley were his first top picks before Bohm). Barber has had a bit more success though not a lot of high picks. Derrick Chung seems to be getting better high end international talent to sign than Sal did though we are probably 5 years away from evaluating his success rate.
Considering trades and lost picks and where we have been drafting the system is doing OK. We are in the bottom 5 in resources but usually closer to the 15-22 range in the rankings. That is not awful. We still trade prospects too (Tait and Klassen and Lee are all top 200 prospects traded in recent years). We are better at developing pitching than hitting but that does not mean our hitting instruction is anywhere near as bad as you portray.