To answer some of your questions:
As to the smallish fast defense, I think that plays in the Pats' hands. A small, fast defense has no defense vs. Gronk. Gronk is near impossible to cover, but if you are going to have a shot you need to out physical him at the line of scrimmage. A defense that relies on its speed is not the defense to defend Gronk.
Plus, Brady has done well against the current regime's defenses:
2011 in Indy: 29 for 38 (76.3%) for 289 yards, 2 TDs, and 0 INTs (Pats win 31-24)
2012 in NE: 24 for 35 (68.6%) for 331 yards, 3 TDs, and 0 INTs (Pats win 59-24)
2013 in NE (his one clunker because no Gronk): 13 for 25 (52%) for 198 yards and no TDs or INTs.
As to the Colts being the highest scoring team in the league, they are averaging one point more a game than the Pats (32.2 PPG vs. 31.2 PPG) and that includes the fact the Pats struggled on offense the first four week. Over the last five weeks, the Pats have scored far more points than the Colts (40.2 PPG for the Pats vs. 30.8 PPG for the Colts). If this turns into a shootout, I like the Pats' chances.
1.) Jamie Collins did very well shutting down Fleener last year. I would assume Browner would see Allen a lot in the red zone. I still think you take away Hilton and Luck is seriously hindered. One of Luck's weaknesses is that he still focuses in on one of two receivers. I actually hope the Pats force him to throw to the TEs. I know the Giants did it and failed, but they are a horrible defense.
2.) The Pats committed to the run last week even though it didn't work. I expect them to continue even if it doesn't work. I think Gray vs. this smallish defense can have a good game. As much as the Pats run defense gets maligned, the Colts are giving up just as many YPC on the ground as the Pats (4.4).
3.) I think people are making too much of the refs. Odds are even if they are flag happy and call a lot of ticky-tack or non-calls, they will not affect the game.
4.) I think there are mismatches on the Colts' o-line. It is not a great line. The question is whether you pressure Luck or you try to contain him. During the playoff game last year, they did bring the heat.
5.) During the playoffs last year, they did bring the heat (3 sacks, 10 QB hits) and held Luck to one rush for 5 yards.
6.) I still think Dobson will rebound at some point, but he is irrelevant. If he can come back and be an actual contributor, it only improves the Pats chances. If he doesn't, it has no bearing on the game. The Pats did well without Dennard against Manning and the Broncos and they have far more weapons.