Having coached both defenses (4-2-5 and 3-3) and I can say this while avoiding writing a whole white paper on the deal: The structural differences inside the box (alignment and assignment) is less significant than on the back end. Ran enough 30 in the 4-2-5 and a whole host of 40 under and over in the 3-3 using similar defensive players. I've said this a ton over the years, if you have the right personnel in your SE, NT/DT and DT, you can toggle between 30/40 relatively easily. Really it comes down to what role you want the DT/NT to play and whether that guy can execute that role. You don't need a 'prototypical' NT to have a great 30 front, but it sure helps. If you want him to be the classic two gap guy on top of the center, and that is how you are going to play your scheme then that guy better be beefy and hard to move. If you are intent to moving that guy around (dropping him, running twists, stunts and sticks) then he probably doesn't need to be shaped like a bowling ball. Beyond that both defenses with different verbiage and philosophies use a flex player on the L.O.S. (rush end/LB in the 30) and quick end in the TCU (Gary Patterson 4-2-5). The two anchor LB inside the tackles are essentially free players w/ little pass responsibilities. Reads are a bit different, but when it comes down to it is the style and substance of what you are having the DL/LB do that creates a clear separation between the two defenses.
I for one prefer the rules of the 4-2, but really grew (with time) to like the positional and schematic flexibility of the 3-3. I used that 3-3 from every thing from a 3-2 Dime to a 5-3 run stopping bear defense with a lot of the same personnel. Just my opinion, but I think there are a lot on this board get stuck on the personnel/alignment and not whether what they are asking the personnel to do within the scheme is executable. That remains to be seen with this group, but the 3-3 at its foundation is entirely capable of handling the personnel and the opposition the Griz will face.
Just my two cents.