Coach, I'll agree with you on that, and the difference, of course, is the top-of-the-line talent at the elite ACC/SEC schools as well as the depth all the way down to No. 35 on those rosters. Even the very best D2/D3's can't come close in that regard. The gaps can be just as big within the D1 level itself, especially if you're comparing a Top 25 program to the back-end teams of a lower-tier conference. And, yet, as you said, on any given night, a lower-tier D1 or a D2 or D3 could give one of the big boys fits, especially if the right guy was on the mound.
Many of the top guys at a D2 are ones who slipped through the cracks or were late bloomers or were players who kept working harder than everyone around them. Some are guys who stepped down from D1 if a particular situation didn't work out for them. Baseball can be inexact when it comes to judging talent, and there are hits and misses at every level when it comes to recruiting.
All that aside, I'd tell dads not to get too worked up over comparing the different levels. Find a program that works for your son and enjoy it. The point should be to become the best D1 player/team you can be or the best D2 or D3 or JUCO or NAIA player/program you can be. Have fun. Work hard. Get better. Eventually, the pro scouts sort it all out anyway.
The point is to keep playing, and I'd agree with all the other posters on here who advise to find a place where there's a true opportunity to play. Don't get too hung up on which level you think you have to reach.