I have a lot of G1 backcards. Most of them are in lever arch files, each in individual wallets. Those that are too big for the wallets are either stacked up in the drawer alongside the folders (ie the boxes collapsed down), or if they still have the bubble, which some of mine do, they're stored inside a MLP Waterfall box (I have both waterfalls, but they both actually fit inside the US box, LOL. I have the Satin Slipper Sweet Shoppe in one of the UK boxes and the backcards in the other xD).
I also have some cards stored inside boxes. The most difficult ones to store are boxes which still have their inlay intact, and sometimes some accessories. So they're on a shelf in my cupboard as though they had the ponies in them. That's only a handful, though - the two princess boxes, Confetti...maybe the newborn twin boxes.
But boxes are a bit more complicated.
If you're dealing just with cards and no bubbles, a lever arch file with plastic wallets is a good way to keep a lot of them safe. I have mine in sets and roughly year order.
G3 cards are smaller than G1 (which is what my collection is) but some G3 boxes have the side flaps. If your boxes still have those and you don't want to fold them down, then that might be a size issue for the wallets.
Regarding different size cards, I don't find this a problem. G1 surprise newborn cards are tiny compared to your average G1 card, but I still have that one in the folder with all the regular ones and it isn't damaged.
I do have some packaging for my G3 but most of it is in a box in the attic with the ponies. I do remember using some of the bags from pony releases to put packaging in though.
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