As you've stated, I believe that the 1) injuries are obviously the biggest wildcard. There's no doubting your opinion that when healthy, we're clearly the cream of the crop.
I do have some major concerns for the 2) running game, though, and your example of the 2012 AFCCG loss to Baltimore is an excellent one to drive the point home. During that game, we had the ball inside of the BAL 35 (normally considered scoring territory) a total of SEVEN times, yet only came away with 13 points due to the windy conditions that were seen that day. Considering that it's Foxborough, I worry that we may see some type of weather conditions which equal the playing field a bit, despite the overwhelming opinion that Brady always gives us the edge. To take this thought one step further, I believe that getting the running game going is a must. Yes, we've seen examples where they played well without rushing the ball, but eventually that is going to catch up to them--or at least that's my concern. A well balanced team like Pittsburgh, Cincy, or even Denver could take advantage of a torrential downpour, which would neutralize our passing attack, and allow them to chew up some clock.
Another thing I've noticed this season is that the 3) turnovers aren't where they need to be. In 9/14 games, we've produced one or less turnovers. We're just not causing enough, and that needs to change. That's not something that we usually see with the Patriots.
And finally, I worry about 4) some weird combination or parts of issues like poor bounces, poor calls, poor weather (sorry to bring it up again), etc. In the postseason, one big play can ruin the entire game, kind of like the 2010 NYJ loss where we clearly played a better game and yet still lost all of the momentum and looked flat. By the time they started to mount a comeback it was simply too late. I don't suppose there's anything that can be done to avoid something like this, but I figured I'd note it in my doom and gloom response.