I use a brush on my AR's. My opinion, for what it is worth, is that boresnakes are good for lever actions and for touch up between thorough cleanings. Maybe it's the barrels I have on my AR's...but the AR seems to be much dirtier (gas system?) than bolt actions, etc., and require more effort and soak time to get clean.
Rastus, Yes, the reason your AR seems dirtier is because the "gas impingement" operating system blows hot muzzle gasses back into the action much like " gas Blow back" (it vents into that little tube at the top of the bolt carrier).
Gas piston systems on replacement uppers run cleaner, AS I UNDERSTAND IT (help me out here guy's/gal )because the gasses cool while pushing the piston back and so do not bake themselves on to the parts.
DPMS's printed instruction say to clean the chamber and bore after every shot for 25 shots, every 10th round up to 100 rounds, to achieve best results for accuracy.
It's a giving I'm following the manufacture's recommendation, so my question is this: bore snaking good enough, or should I actually get in there with a brush?
I'm new to this, and believe the only stupid question is one that goes unasked - so I'm asking. 
To get back to the OP, I would use a brush, again this is only my understanding of it and could be wrong, (heaven forbid !

) But what you are doing with the "break in " period is smoothing and more or less honing the inside of the barrel. Machining raises burrs and small flakes of metal, it also disrupts the way the metal molecules lay in relation to each other, the "Break in " process brushes them into line and smooths out the minor irregularities caused by the force of being machined.
An example of this , when I used to do "Sheet metal Fabrication" all our aluminum parts were run through a flat sander before forming, some alloys if run parallel to the bend line would crack, as the molecules were separated, but if sanded at 90 degrees to the bend there was no problem as each molecule would bend and no stress was placed between them.