I would support AFD on DPI, UNS, and personal fouls by the defense (RPS, UNR (IPC in NFHS), HCT, TGT, LTO (late hit out of bounds), etc.). This would remove the differences between NCAA and NFHS in that regard. I would also abolish illegal participation, because this penalty is infrequent, and is often caused by officiating errors (As an aside, how does NCAA adjudicate a player participating with his helmet off?).
I would be on board with the 12/3 (EBO does this anyway in their games) halftime rather than the 15/3 halftime, throw away outside the pocket being legal, no NZ after the ball leaves, etc. No visible play clock would not be an issue for 40 seconds if the BJ (or other official timing the play clock communicates that play clock starts, 25 seconds, 10 seconds, and the end of the play clock. This is how I and my partners on semi-pro games have communicated the play clock (semi-pro games use either college or NFL rules, and those rules include a 40-second play clock).