A little off topic, in the video that Nickle posted, I saw the comment about "elevating WRs like A-Rod or Brady can". Brady didn't start putting up eye popping numbers until they brought in Randy Moss, then followed with the Hernandez/Gronk duo, and now Gronk by himself. Over the last few years, we've seen how different New England's offense is without Gronkowski.
Rodgers, is a better QB than Brady, IMO; at least from a physical standpoint. Rodgers has a better arm, more athletic, etc. He also has not been exactly bereft of talent during his days in Green Bay (Jennings, Driver, Nelson, Cobb, Finley, etc), with many of those guys being there for consecutive years at different points. It also helps both Rodgers and Brady that there has been no change to the offensive system their entire starting careers. Both GB and NE have changed coordinators but not their offense. Consistency is key.
Back on topic, I think when dealing with so many factors on the offensive side of the ball; injuries, new/inexperienced players, new system or at least a tweaked system with new terminology; you're going to need time to develop things.
When you're running out an undrafted guy, a journeyman, a guy off the P squad, a cast off from the Rams, rookies at TE and a 6th rounder who played in a triple option, you're inevitably going to see issues with route running. Whether it's in regards to precision, timing, getting proper depth, knowing when to sit down in zone or flow away from coverage, etc; there are going to be problems with consistency and execution. As a play caller, you probably try to simplify things for your pass catchers, which means quick outs and stuff to that effect.
Perhaps as the running game gets on track, as we get healthier and guys can some experience in the finer points of the game, we see an increase in the use of the middle of the field. Combine that with Flacco being confident that guys are going to be where they're supposed to be based on his read of the coverage.