I don't think he looks to skinny. With a GSD you should see the ribs or at least feel the ribs. It is normal for GSD to have a waist line. People accused me of starving Fiona because of her tapered waist. But coming here I was assured she was normal. What does your baby weigh? A vet visit isn't a bad idea.
He looks great to me. A vet would be able to better assess. I can't give input on the amount of food because I always free feed unless it becomes a problem. I would definitely say your dog doesn't look sickly.
Put the 3 cups out. If he eats it all up, the no more til the next day. I free feed Fiona. Put 2 cups out in the morning. Usually not eat much. Then at dinner eats some more. I put one more cup out. When I get up in morning usually gone.
He looks fine - if anything, a little thicker than my pup at the same age.
Everyone who doesn't own GSDs think the pups look skinny, when really they're just that way at that age. They fill out when they get older. Make sure your vet checks him for worms and keep track of how much weight he gains. My boy put on about 9 pounds in 3 weeks from 10 to 13 weeks old.
I free feed him - he's growing fast and still looks skinny, and his food dish is always full. But there's nothing wrong with feeding him a couple of times a day if that's what your schedule permits.
The link below will take you a a condition score chart which will take you through how to tell if your pup/dog is over or under-conditioned. This is the way that vets get taught to assess dogs. I cant really tell you he's too skinny without feeling him so this will be really useful for you.
I prefer not to free feed with any puppy that is a large or giant breed. I don't know what you feed him but the recommendation is to feed a specific large breed puppy food and follow the amount guidelines on your package. This is because excess calcium and/or energy intake in large/giant breed puppies can lead to developmental orthopaedic disease. That said you will still need to assess your puppy (using the chart) and alter amounts accordingly.
Sorry If I've told you anything you already know. If the link doesn't work just google 'Purina body condition system'. Hope that helps!