Why is my 3-month GSD puppy so fearful and cries when I touch him?

At 12 weeks, I highly doubt that Cortes has developed a severe dislike or fear of any particular person since my assumption is that you were his first owner. He may just be a fearful puppy that is going to require a lot more work and patience than the average dog. The other possibility is that there is a physical problem that is causing him discomfort whenever you try to contact him. If he is in some sort of pain for some reason, he may even be anticipating the contact and reacting to it beforehand. GSDs are one of the most dramatic breeds and are much more likely to act like that and do things like that than your average mutt. If you are able to rule out that there is no physical issues for sure, than I think you should consider contacting a trainer right away. Most trainers will work with you as long as your pup is at the very least Rabies vaccinated. I would stay away from puppy classes for the time being, instead using a one-on-one trainer to help you out. In terms of things you can do at home, Cortes needs to be continually rewarded for the behaviors and actions that you desire most. In a case like this, you have to take baby steps. By this, I mean if he even starts to make steps in your direction without a negative reaction, he should be rewarded with praise and treats. A bigger reward should be given for even great accomplishments. I think teaching the touch command in this particular instance would be a great idea. This will allow you to communicate with and play a game with Cortes without actually having so touch him physically. The idea of the game is to have your dog touch his nose to your hand or to an object of your choosing. There should be many different tutorials and videos all over the internet that will show you how best to teach a dog this effectively. I know it's hard and it sounds like Cortes might be harder than others, but don't give up just yet! It's all very new for the both of you. Hope this helps!