I'm sure the Pats will offset any deficiencies from QB play by adding RB power, extra WR's for short-yardage completions, and keeping their defense's football IQ unnaturally high.
Even without Brady, I don't see the Pats being a pushover. They're an extremely well-coached team and they make the necessary halftime adjustments. To OP's point, I think the Fins can definitely defeat them in the coming years, but Miami needs to be on it's A game. I think how Philbin performs as HC this upcoming season will dictate what the current Dolphins are made of; it's his time to try and out-coach Belicheck on an even-talent plane.