You need to consider sample size.
We were 8/13 on 3rd down, so I don't know why play selection on 3rd down is a concern.
I haven't looked, but how many 3rd were short enough that a run would be appropriate. I think the whole league throws 90% of the time on 3rd and more than 2.
3-1-NE 36 (13:29) T.Brady up the middle to NE 38 for 2 yards (M.Spears).
3-1-DAL 29 (1:19) (No Huddle) T.Brady up the middle to DAL 27 for 2 yards (J.Ratliff).
3-4-NE 23 (5:08) (Shotgun) T.Brady pass short right to R.Gronkowski to NE 31 for 8 yards (F.Walker, A.Elam)
3-4-NE 28 (3:52) (Shotgun) T.Brady pass incomplete short middle to A.Hernandez [S.Lissemore]
3-5-DAL 25 (10:02) (Shotgun) T.Brady pass short left to W.Welker pushed ob at DAL 12 for 13 yards (O.Scandrick)
3-5-DAL 29 59) (No Huddle, Shotgun) T.Brady pass short left to A.Hernandez to DAL 21 for 8 yards (O.Scandrick, A.Ball).
3-6-DAL 8 (9:01) (Shotgun) T.Brady sacked at DAL 13 for -5 yards (D.Ware).
3-6-NE 48 (3:29) (No Huddle, Shotgun) T.Brady pass short middle to R.Gronkowski to DAL 44 for 8 yards (A.Elam).
3-6-DAL 40 (2:18) (No Huddle, Shotgun) T.Brady pass short middle to A.Hernandez to DAL 39 for 1 yard (O.Scandrick).
3-9-NE 22 (15:00) (Shotgun) T.Brady pass short left to D.Branch to DAL 33 for 45 yards (G.Sensabaugh)
3-9-NE 38 (10:35) (Shotgun) T.Brady pass short middle to D.Branch to 50 for 12 yards (M.Jenkins).
3-16-NE 32 (12:04) (Shotgun) T.Brady pass incomplete short middle to W.Welker [J.Ratliff].
3-18-DAL 18 (12:52) (No Huddle, Shotgun) T.Brady pass short right to B.Green-Ellis to DAL 7 for 11 yards (A.Spencer).
I don't see a lack of rushes on 3rd down as being a problem in this game. I was a little disappointed that there were so few screen plays called since it looked to be a good counter for the Cowboys jamming the middle.
An interesting point for me was the fact that the Cowboys next-to-last drive was the first time all year that an opposing QB took a snap with the lead. 3-n-out. 2 negative runs. 0 net yards. Punt with only 1:05 (and 2 timeouts) taken off the clock. Big-time stand by the defense. But to be fair, the Cowboys were hampered by their coach having his hand up Romo's anus (and his head up his own).