With all due respect, in the last several games teams aren't running on the Patriots with success. However, they are passing on them (in the first halves anyway -- especially middle and those MF crossing routes). So unless you mean you are worried about Ajai and Blount wearing the Patriots down from catching passes, the concern clearly is the Eagles converting third downs through the air at too great a percentage (I'll be happy to see handoffs to A & B).
There seems to be a clear pattern: Game starts, Q1 and Q2 we seethe D be mostly too soft, O is too sluggish. As the game progresses the D gets stout and the O gets it done. So I'd say concern #1 is, does the pattern persist -- D gives up third down pass plays and O can't concert 3rd downs -- and is the hole it creates too deep to get out of?