The NCAA setup I run (Described here -
https://forums.ootpdevelopments.com/...&postcount=111) has a high school feeder league with 610 schools that produce about 3000 high school seniors each year for the MLB draft. About 500 are drafted (plus another 250 from the NCAA). The undrafted high school seniors, and those drafted high school seniors who elect not to sign, are then available for my NCAA recruiting process. The 142 schools only need about 1200 incoming freshmen, so the numbers work out pretty well. The system doesn't bog down. To Syd's point, there are, on average, only two players drafted in the MLB draft per school, but that hasn't been a problem (your Longhorns and Trojans get four or five drafted per year and your Butlers and Valpo's usually don't get anyone drafted). OOTP even does a nice job of retiring some Juniors who don't see a path to the pros and maybe haven't been getting a lot of playing time, making their senior year a waste.
So the current OOTP feeder system can work to support a playable NCAA setup. it will still take some programming effort from Markus and the crew, but the current engine would support it.