I've used retro game cases for some N64 stuff, they all turned out fine. Depending on the unique nature of your labels, some Etsy sellers will reprint your artwork for other customers if you don't tell them not to. So just be aware of that... Here is the info for retro game cases:
https://www.retrogamecases.com/a-detailed-look/labels/
As far as not putting the label on the games, you own them - do what you think looks best. Maybe in the MegaMan 2 proto, carefully peel the label off and keep it in case you decide you want that look back? Labels aren't permanent, you can change your mind down the road.