This part of the description stood out to me: "will likely start all 4 years at their chosen position."
I would never make that assumption at any program, especially at D3. If the new coach is going to turn things around, he's going to do it primarily by finding better players. Sounds like school "A" has a track record of developing guys and playing more juniors and seniors. School "B" has no track record, so there is some risk involved. School "B" may still be the better choice, but understand the risks.