The recent trend in the NFL has been to faster, smaller LB's. Denver has three good ones in this mold.
Note that the Pats are countering by running three-TE sets. The Pats can come out and run straight at the LB's, negating their speed and making this a battle of strength and leverage. Run inside the numbers at this type of defense. Battering them with Graham and the guards should be fun.
I agree that throwing to the tight ends will be tougher against these linebackers and safeties. I can't see how simply switching Thomas for Watson makes it easier for the Pats simply because 'they haven't studied Thomas.' He's just a slower, slighter TE than Watson.
Bailey is an excellent corner, and they have a couple good young emerging corners - their drop from two to three isn't much. Brady is going to have to have a better rapport with the Patriots receivers to beat this defensive backfield. And again, screens are tough against a speedy linebacker group like Denver's. Some outs, curls, those routes can beat the Denver corners.
On defense, the Denver backs are clearly a step below where they've been historically. The OL may not be at its peak, but the system still works well. The DL is going to have to be careful, and, as noted, the LB will have to stay in their areas of responsibility. This is the kind of game where Beisel could get killed, but the discipline of Bruschi, Vrabel, and hopefully Seau should work well.
I assume you put Samuel on the bigger Walker and Hobbs on the craftier Smith. Hopefully the line can continue to generate pressure and force Jake into mistakes. Early pressure can really frustrate him, with Cutler waiting to offer him the clipboard.
You have to imagine that the Patriots will be as geared up for this game as any all season. The Branch crap is behind the team. They played sort of crappy in their two wins against weaker teams. Brady is finally getting a chance to work with the receivers he's got for the season. The running game is coming together. The team has the stink of last year's loss still on their minds.
Can't wait.