One of the things that hurt Bill Lynch is that he had far less tolerance and willingness to overlook bad behavior than Hep. I don't mean this to trash CTH or to speak ill of the dead, but Hep was never regarded as much of a disciplinarian. I personally knew a couple of guys who coached with him who both shared the opinion that he was a great guy and a great coach, but that he had a bit of Bobby Bowden and Joe Tiller in him when it came to disciplining star players. I also know a kid who played for him at Miami who talked about the shenanigans that Ben Reothlisberger got away with there. Some of the rumors regarding his bad behavior in the NFL aren't hard to believe given the stories that this kid told.
Kellen Lewis and James Hardy both crossed lines that Bill Lynch wasn't willing to tolerate (and in fairness, Hep might not have either). Booting Lewis and suspending Hardy (who left early in part because he was in Lynch's doghouse frequently) absolutely hurt Lynch's success as head coach at IU. Coupled with the fact that CBL's less-than-dynamic personality hampered his ability to attract top-tier talent to IU kind of ultimately doomed him. I still maintain that Bill Lynch was as good a strategist as any coach we've had since Bill Mallory and I defend that based on the fact that both Mallory and Hep actively sought him to come to IU as an assistant. Unfortunately, the ability to attract ample numbers of top-quality talent is an essential part of being a successful P5 head coach.