Totally agree and there are a top set of D2 that have solid academics. D3 will of course go much higher academically. I think the main concern is the amount of time to develop and practice at a D3 is more limited - especially in the fall.
Dad,
I might suggest looking at the overall for your son in a more global sense going forward. This would include, as you already are, the baseball and academic sides of the college experience. If your son progresses next Spring as you are hoping, he may well open additional doors, but the doors might not be coupled with educational opportunities of the type you are suggesting to be very important. I would anticipate the baseball coupled with the top academic side will be mostly developed by the end of 2017. If this were my son, looking in the rear view mirror, I would think a top academic/great baseball opening occurring next Spring would be fortuitous at best.
Two aspects of the global approach which seem to be missing or confusing to me, at least, from the thread, so far, are the definition you have for "development" at the college level and, perhaps equally important, Summer Wood bat league experiences and options.
Our son was one of those D3 guys who developed through his college program and was drafted. The D3 is one which is at the top of the D3 baseball programs coupled with academics which (at least in Texas) are viewed as comparable with those at Rice.
One reason he was drafted (as a position player) was the development he received through his college program and coaching staff, which runs their program very much like a D1. D3 Fall ball can be very different from region to region and even conference to conference. Development is not always on the field. Part of it includes the strength, flexibility and other "explosive" aspects which are critical in college. Being aware of the type and success of strength and conditioning program is too often overlooked.
A second aspect is location. The I-35 corridor is covered with MLB scouts and our son's D3 coach had scouts looking at our son from their very first scrimmage his freshman year. Coupled with top academics, if you feel your son can compete, then he would need a coaching staff which will give him visibility to the MLB scouting community in ways which highlight your son. There are plenty of coaching staffs from D1-3 which do not get this done in ways which are effective.
What is really missing from your assessment thus far, though, is the Summer leagues. Having a college coaching staff which can place your son in either the very top leagues or in the very top teams of that tier of leagues just below the Cape can be very important if your son does progress and has the potential by the time he is a junior in college. If your son is a lefty throwing 90 by the time he is a junior in college, he is going to get discovered. If he is below that velocity, Summer leagues can be very important, especially for D2 and D3 players/pitchers. As an illustration, the D3 program where our son played and later coached gets regular placement in the Northwoods, Coastal and NECBL and very occasionally in the Cape. The return on those getting drafted is pretty impressive at the D3 level.
If you are hoping to provide your son the best options if he progresses through his junior year in college, Summer league placement is probably a very important part if your son ends up at a less than top 75-100 D1 or a D2/D3.
Good luck to your son. I hope things work our well for him. The great insights you have received from those who already posted should help him considerably.