This is what I'm thinking as well. I think the reason we had a lot of those blow outs last year was because the players were young and couldn't grasp the "fundamentals" of the offense. I think Butch and co have a system that says first this or these plays then those then these until the whole play book is open and any play can be called with faith in the players that it will be executed.
Actually it is more than just grasping the fundamentals.
IIRC, someone posted a fairly long article here once that explained Jones' O approach. It IS built on "trees" both in the passing and run games. You have a based play then a succession of plays based off of that base play. When installing that kind of a scheme, you have to master the base plays and their immediate variants before moving to the more complex stuff.
I think the word you were looking for was "master" rather than grasp. The team has to "master" one layer before another is added.
However, if this is true of Jones then we SHOULD see improvement this fall since a system that requires more than 2 years to master... would be fairly useless when players rotate out of the system every 4 years.