All three have their problems.
Carton - Hardest to find in good condition and made of cardboard.
Old Case - Trays cracks and sometimes the plastic lining shrinks and causes whitening on inserts. I do like how they open and how they smell like vinyl. It is like opening a new game each and every time you open one up
Snap lock case - Causes indentations on the insert due to crevices and snk embossed logo (both which can be fixed through a acid free paper cut to the right length underneath the insert). Additionally, the snk logo inside the case likes to scratch up the back of carts (can be fixed with bubble wrap). Another point is that if you are not careful, you can break the snap lock right off (I always make sure to have one hand on the back of the snap and one to open to make sure I use the least amount of pressure)
I am going to go with snap lock cases on this. Wanna know what they all suck at? Holding the manuals.
Just a feedback here.
I went through all of my AES games with snap lock cases over the weekend - checking for conditions/moisture buildups.
When SNK first published games with it (1995 - Fatal Fury 3), the case comes with mat finish surface. Great, but when it wrinkles it's so obvious and worst of all it causes the inserts to wrinkle, especially games with tight slack. This is more apparent with DG's reproduction cases for NGDEV releases. All of my games with this type of case (early 1995 - early 1996) have arched wrinkles on both sides of panel, just depends on how severe it is.
Starting 1996, SNK perfected the art by switching to vinyl/shiny finish surface, problem solved. However, SNK still didn't solve the issues of SNK logo causing carts to scratch.
Shockboxes:
OK, it's for MVS but this has issues too.
When you try to put inserts into them, do not bend the cases all the way (180 degrees) as the bottom of the side panel will crack open. The inserts are very hard to slide into, fortunately most MVS inserts are very wrinkle/bend resistant, unlike the original SNK AES inserts.