Honestly, I'd prefer Josh make the short throws and keep the clock moving and drives alive etc. As watching Brady and Manning to me that's how you win. Bombs are great but sustaining a long drive to me is football at it's best.
BB as a HC is like most defensive minded coaches in he likes to keep his team in the game aka within one score and then count on his QB/team won it at the end or his D/team stopping you. No QB is as clutch as Brady and why they worked so well together. That said BB as a GM is really bad finding offense talent at WR and TE and when you don't have a Brady guy that makes everyone else better your offense is weakened even more. I don't know when his contract ends bit wouldn't be shocked if he walks away when it runs out.