Read the first part of this entry. The O-Line isn't playing as well both in pass protection and running the football. Although the level of defenses they seem to be playing this season are also better than last year as well, so there are a variety of issues in play here that are part of this overall problem.
Without reading the article yet Ian, I am guessing that some of the problems and differences are:
--the fact that we have moved away from the "quick timing" 5-10 yd passes in the slot which allowed Brady to have the quickest release time at one point last season. One thought is that this may either be a pre-planned move, or they simply haven't been able to take advantage of Danny Amendola due to his injury problems so far. This surely made the offensive line look better and hid some weaknesses, just as we're seeing with Manning (It's nice not having to differentiate what Manning I'm referring to anymore)
--the lack of balance/success in the running game, as this too hid some weaknesses. As noted in the post above, the magic number for Brady pass attempts is under 40, as we are 21-2 since the beginning of 2011 when he passes for 39 or less attempts. This of course, leads to running the ball more. Our offense as a whole actually scores more pts on average during this period too, with a 34 ppg average. In comparison, we are just 9-7 in games that show 40 or more passing attempts, and average a full TD less at 27 ppg
--the tendency to have both QB and WR seeing different things in the defense, which has led to miscommunication problems with the rookie wideouts. This has led to having to hold the ball longer for Brady, which in turn exposes the weaknesses that we already had on the offensive line last season (RG--Connelly was often viewed as the "weakest link," and C--Wendell was likely the second weakest)
--the change in philosophy from the TE targets. Prior to Sunday's game we had targeted the TE position a whopping total of 15 times. Hopefully that changes with a healthy Gronkowski moving forward
--as mentioned, last season we were already having to deal with issues on the center/right side of the line, and those issues are clearly being exploited now due to some/many of these factors named above. This brings up a whole new issue of whether or not to extend Wendell and/or restructure Connelly's overpaid 3 million dollar cap hit in 2014. These issues will also coincide with our need for drafting an interior lineman in the first few rounds next spring, possibly even in the first round or two--and possibly even taking a "double dip" on the position of OL altogether, much the same as we did with front seven, RB, TE, and WR in the past few seasons