Well
1) standing up vs 3pt stance makes a difference
2) 4 of the front 6 are, in fact LB's - you can argue Neal is a hybrid, but he transitioned to LB very well I thought, and dropped some weight to do it - as a result that defensive front is small and routinely gets blown off the ball on run downs - and since Capers plays the 2-4 on run downs, it happens far too often
3) 2 of the 4 LB's in Capers 2-4 are Hawk and B. Jones - both of whom are weak links in our defense; and while those 2 weak links are left on the field, more talented defensive linemen are twiddling their thumbs on the sideline
To make better use of the personnel he's been given, he needs to design schemes that put the DL on the field in pass rush situtions, and use the space eaters, i.e. Boyd, Guion, Jolly, Worthy, et al, in a base 3-4. In the nickel, the best way to get the most talent on the field is to go with a 3-3.
It isn't that complicated.
It's not, but I think you're making it more complicated.
1) Yes and no. It's probably a wash. They give up some leverage for more visibility standing up.
2) Ignore that they "are linebackers." Look at their heights and weights. Perry, Matthews, and Neal are all big enough to be designated pass rushers in 4-man nickel front...
3) Which is what the 2-4 and the 3-3 both are. They are nickel fronts. You're going to give up run defense when you run nickel. It's a balancing act.
There is no promise that the 3-3 would be a better run defense. It might end up being worse. I'm not saying it's a given, just that it could happen.
In my mind, a 3-3 with the current roster would be something like Daniels on the nose, more than likely shaded (1 technique--he's not really big enough to two gap, so set him up for pass rushing success), Neal as a three technique to the weak side, and Peppers as a five technique to the strong side. I'd probably want to blend size for outside run defense, so put "small" Matthews to the same side as "big" Peppers, and "small" Neal to the same side as "big" Perry.
Diagraming this out, I still see a natural running lane up the middle. Having two inside backers might give up more short runs, but fewer longer runs, because you have more bodies that can move, scrape, and run down backs.
EDIT: I just found something else I don't like about the 3-3 with our roster. Man-to-Man coverage.
Let's pretend the offense comes up with a 3WR, 1TE, 1RB set. Pretty basic stuff. Packers go nickel to match up one CB per WR. Play call is a simple, straight up, cover-2-man (two safeties playing deep halves, CBs manned up on WRs, 1LB on the RB, 1LB on the TE.)
And there's the rub. You need two coverage capable linebacker on the field. Matthews and the MLB in this scheme (Jones or Hawk) would be adequate, but now you've taken Matthews out of the rush. Who else on the roster could do it?
As a change up, that's awesome--let the offense worry about Matthews and the drop him out. If that is your gameplan, you've made every other offensive coordinator in the league happy. Like 5 year old on Christmas morning happy. All he has to do is shift the TE to Matthew's side and he's "blocked," because now he's in coverage.