I'm not extremely experienced with making patterns, but I have made some stuffed animals and clothes from my own design. I've never used an actual store bought pattern. I'm lazy and irresponsible like that.
When I'm making a stuffed animal, I first sketch how I want it to look and where I want the seams to be.
Then I draw what I think the flat pieces of material should be that would fit together into the 3-D shape. Because not all edges will have the same shape as the edges they match up to, I use a piece of string to make sure that the bottom of a duck, for example, will match up to the sides, even though the curves in the pieces of fabric are slightly different.
If you want the joints to be round, make sure the holes in the yellow shell are round where they attach to the limbs. If the hole was a slit instead of a circle, the joint would be much more flat.
Even using a thin material for a "see through" look would be a pain, I think. It'll show the stuffing, not the black body, and if you leave it unstuffed, it'll be saggy. One option is to use a thin cotton for the shell and to paint (in very very watery acrylic) the body onto the yellow shell so it looks like you can see the shadow of the body.