I'm not sure how these issues are to be rectified. Obviously there's not much that can be done this season; just have to win out, and to peak at the right time.
Going forward, it's hard to imagine things getting better anytime soon. Brady is getting older and seems to be showing his age in some regards. There isn't much salary relief in sight, and there aren't an abundance of draft picks to restock the team.
It's unfortunate that the team is in this situation at this point in time, with Brady's career coming to an end within the next 2-3, maybe 4 seasons. Ultimately Belichick has himself to blame for that, but I suspect he never intended to construct a great team right now for Brady specifically. His formula will not change, and in part that's due to him wanting to have the ability to compete following Brady's retirement.