What do you think is the better way? Doing specific exercises like med ball tosses, rotator cuff work and so on or general compound exercises like squats and deadlifts?
I think a lot depends on the strength level. The weaker you are the more strength gains are going to carry over to baseball and general compound exercises build strength the best.
For example a weak kid that throws 82 but only can deadlift 150 pounds will gain a lot by raising his deadlift to 300. He won't gain much strength by doing specific exercises.
But a guy that already deadlift 300 will gain much less for baseball by raising it to 400 pounds. That guy might benefit more from specific exercises because his general strength is already good.
Eric Cressey has warned against certain exercises like the back squat, power clean and bench press due to loads to body parts that are sensitive with baseball players but then again not much harm can be done squatting 150 pounds. However if you get above 350 or so the loads do get big and it might make sense to search for alternatives.