Manuals are a thing of the past. Sure, I love manuals as well but in all honesty? I only read them once and never again will I see them.
Also, regarding the size of vita cases, they are already extremely small. These cases can easily fit in some pockets, any smaller would be bad. Those stores that put the games where the customer can access it, is easily taken and stolen. Also, if you have cases as small as the cart itself, it'll have no presence whatsoever and will be easily overlooked. Vita cases probably has the less plastic use of them all, so it's fine as is.