Not too fond of using zip bags for storing keycaps. I'd prefer a method that can display them in all their glory.
Believe me, I tried every solutions I know. Cheap trays, expensive custom acrylic trays, transparent plastic box with dividers, keycap paper with 3M double sided tape... Every solution has its own problem and nothing works as good as Ziploc bags.
Later I bought zipper bags in several sizes. I separate my keycap sets/kits into different bags and then put all of those bags into a large carton box. I'm happy with that now and will never think about another keycap storing solution again.