I think the main issue for the offense is they really need to establish a short/medium passing game, which they really had very little of last night (and even less once Amendola went out). I agree with others who have pointed out they simply don't have a reliable slot option as long as Amendola is injured, so they need to be more creative. They may need to revert (to some degree) to the types of offense they had in the earlier years of the Belichick/Brady era, with more screens, dink-and-dunk passes, etc. Brady is simply not at his best (as we saw clearly yesterday and have seen in other games) when they go full Flacco and just chuck everything downfield.
Specifically I'd like to see Burkhead get considerably more snaps on early downs as I think he is versatile enough to do a number of things; they can motion him out wide or into the slot, they can just keep him in the backfield and run with him, can do a RB screen, etc. This is also true to some extent of White/Lewis as well, of course, so it was strange that they largely seemed to treat both of them as standard RBs, with White targeted only 5 times all game and Lewis targeted 0(!) times.