2007 Super Bowl: Mankins had a torn ACL, Brady was playing on a ****ed up foot. Neal left the game with an injury, and the difference was pretty stark once he was gone.
2011: Gronk might as well not have played at all.
Not really excuse-making, just an acknowledgement of facts. Yes, injuries are part of the game. No, that doesn't mean that we have to pretend that a poorly-timed injury isn't a perfectly valid reason for a team performing way below its ceiling.
Also, style of play matters. No matter how you construct a team, it will be susceptible to being attacked in certain ways. For years, the Patriots were susceptible to defenses that could generate consistent interior pressure without blitzing. If it hadn't been that, it would've been something else. In 2011 and 2007, it just so happened that the team we played in the Super Bowl had strengths that matched up with those weaknesses.
Did the Patriots take longer than they should have to address that specific weakness? I think so, although I like the steps they've taken over the last two years quite a bit. Better late than never, and there's no way the Pats win SB49 without Stork in particular. And to be fair, they deserve some credit for addressing that weakness in 2011 by adding Waters. But in the end it didn't change anything, because by the time the Super Bowl came around the second most important player on the team was playing on one leg. Bummer.
But again, just to reiterate: in the salary cap era, every team is going to have weaknesses. Everyone is susceptible to something. The Patriots are far better than most about being aware of that and minimizing their weaknesses. They approach the draft and FA proactively, and a lot of the time succeed in fixing these would-be problems before they even become problems. But sometimes they can't, because the cost of doing so would just open up other problems elsewhere on the roster. Hence the current state of the DBs.
It sucks, but that is just a fundamental reality of the modern NFL. It's not like the Pats are going full Colts and just ignoring the huge, fatal flaw in their roster construction even when they have clear, simple, cheap ways to fix it.