My previous dog (a rough Collie, now living with my parents) was the runt of the litter of 6 pups. Based on the fact we wanted a male and a medium drive dog, we actually got to pick first out of the 2 suitable males. Interestingly the other male was the largest pup in the litter. My parents were dead set on getting him because the dog we had before that was very, very sickly (epilepsy, eventually kidney & liver issues, had to be PTS at around 8 years old) and they were convinced that larger pups were healthier.
When we went to see them, I fell in love with the runt. Yes, he was little, but he was REALLY feisty! Just ran circles around his siblings, was fearless and very outgoing. I knew immediately he was the one and it took some convincing but my parents finally relented.
Samson is now over 12 years old, so for a Collie, he is ancient and living on "borrowed time." He is now very slow and very deaf, but otherwise, such a joy. This is a dog who wasn't sick a single day in his life (despite us paying monthly for "platinum" dog insurance!). His older brother had lots of health problems and died two years ago. Samson is the last surviving dog from that litter and the best dog I've ever come across. If my new GSD puppy was half as great of a dog as Samson, I'd be thrilled!
So don't be scared of the runt, they can turn out to be the very best!