"Can't defend the run"? You better go back and check the tape, and not just the height and weight. Situational player year 1; full time player year 2. Many elite edge rushers have done just that. Take Aldon Smith, for example. Please feel free to predict when Peppers will hit the wall.
McCarthy has already stated on a couple of occasions he plans to use Matthews in the middle again this season. I don't think many are aware that was primarily in nickel last season. That alignment puts "edge rusher" squarely in the needs list. Perry and Neal are merely serviceable; both might be gone along with Peppers by 2016.
Datone Jones is a situational player because, quite frankly, he's not all that talented or not sufficiently aggressive, take your pick. I though Thompson reached for length (pun intended) with Jones, nor was I keen on the Perry pick.
Why would Thompson need to trade up for an ILB? Since this is a rather peculiar opinion, since it should not be necessary step, you must have a specific name in mind.