A 3D inventory is one of those things I've been struggling to articulate, but I'll share some of my ideas thus far. I would love to see it implemented in something, if only to learn from that and see how to make it work best for future endeavors.
To start, I'm in favor of all items being visible on the character at all times and having this influence other aspects of the game. I think organizing items on a character would be just as important as organizing items in a bag (to be clear, I think both should be in the game). There could be certain points on a person's body where items can be placed based on whether that person has the proper means for carrying it.
For example, if you want to equip a gun, you need the right holster. The holster can be strapped to various parts of the body (it would be made clear by a transparent image of places on the body the holster can go, and you can drag and click it in place). If you don't have a holster or the right holster, you can only put the gun in your bag or hold it (as in Max Payne 3).
This can be done with other items, of course. Ultimately, the player should be able to drape, hang, attach, and equip just about anything to various parts of their body. Modifiers would be what the player is already holding or various cybernetic parts.
On top of this, the player can also have a bag that indicates how much space and weight it has available. The weight of course would also be affected by the items your character is holding that aren't in the bag. I haven't given much thought to how organizing the bag would work, but I imagine it would operate in a similar manner, only with a slight change in the details.
At least, this is how I would do it if I were designing my own RPG. I don't know how it would work in the ones that CDPR has planned.
This idea is also related to my ideas for how character customization and crafting should work. Ultimately, I think the player should be given the tools to create what they want (as long as it remains consistent with the given world and game, of course), rather than relying on pre-made item/character models that are limited by the resources of the development team.