College is about the whole experience; not just on the baseball field. I would advise kids to find a school where they will enjoy being a student, their social life and everthing that helps them grow into a productive adult.
The fundemental difference between D2 and D3 is in their ability to offer athletic scholarships. All institutions have the ability to offer "merit" scholarships. With that said; for many a qualified student there may be far more aid at maby D3 schools.
Good D3 programs can compete across the board. That is not to say they are the same as D2 or D1 programs; but the game does not change.
My son choose a D3 program because he did want a good academic program; the net cost was less from the D3 program than the D1 program with baseball money and most of all he wanted to play.