A few things about Mallet.
It is without question, he possesses the skill set of a 1st round talent, he fell to the 3rd.
I would like to gamble that, it was at that time, that the system BB built, "The Patriots Way," forced the team to talk about the not to distant future in the draft war room, and how it might be closer than any of them would like to accept. It was at that moment that a trigger was pulled which would put into place a game plan for a NE team without BB. From that moment going forward Kraft had to look at building a new dynasty and it was BB who showed him the road by proposing the Mallet pick.
In picking Mallet the team would have to carry 3 QBs, they were forced to loose a roster spot. Not only that but they give up the ability to draft a player who would compete to be a starter on the team. Mallet was not going to take anyones job, he was to sit the bench and learn to grow as a player. After loosing the SB, that roster spot looks like a SB ring to me.
The above describes the Patriots Way, team building is done by growing talent, and that isn't exclusive to just players, its true for the coaches.
In comes Josh McDaniels, anyone want to perceive this move as anything other than bringing back home grown talent. I don't think Kraft or BB know when BB would retire, but one can't claim that this move doesn't give a home grown talent the ability to compete for the starting job.
I am not saying that Josh would be given BB's job, but it puts in place a person who can compete for his job. Its important that he is on the team. It would make for an easier transition. It is something Kraft take pride in.
So now with that all said. Why would BB and Kraft, want to deconstruct a good thing. No one knows if Brady would want to retire with BB. No one knows when BB would retire, but planing for things is the Patriots way.
If and when the current plan changes, things will be done to try to achieve the same goal, but at the moment, there is no immediate need to complicate thing. We were in the SB after all. Meaning Mallet isn't going anywhere this year.