I have a concern with designing a stuffed toy which is that over time, if stuffing gets displaced from a particular region like an arm or a torso, it will be permanently deformed since the only way to move the stuffing back precisely would be to physically cut it and resew it which I wouldn't be around to do. How do I make sure stuffing always stays in place? Or otherwise what other material options are there besides fabric and stuffing?
One way to prevent displacement is by making sure the stuffing cannot move anywhere. If all basic shapes (limbs, head, torso, &c.) are separated from the others by an internal wall or membrane, you will prevent the filling from moving outside their limited volume.
Use pre-shaped filling
You can alternatively adapt the stuffing to the final shape of the volume it will occupy.
You will probably have to adjust your technique a little, since this requires adapting the shell fabric around the stuffing, and sewing it in place.
This will have consequences for the tactile qualities of the stuffed toy.