I'm certainly no expert, but I wouldn't worry much about the size difference, I'd focus more on the temperament. I like to spend some time with the puppies and their parents. Though puppies in a litter will vary in terms of personality and even temperament, the temperament of both parents can tell you a lot. Are they friendly, reserved, aggressive? I personally don't like a dog that's too friendly, I prefer a more reserved and watchful demeanor, at least initially. But I would never choose a puppy that was shy and uninterested.
As an example, my puppy's dam barked when we arrived, but quieted once the owner/breeder told her it was okay...then she was all about playing ball. She did not approach me for pets, or offer me her ball, but came up very close without any hesitation or concern. The sire, barked a little longer, but also quieted when told. He approached also without hesitation, and was quiet and non-threatening, but never took his eyes off of me. It wasn't a hard stare, just watchful reserve. If he had been as ball happy and unconcerned as the dam, I would have walked away.
I was in a similar situation to yours in that there were only 2 puppies left from the litter, one male and one female. I chose the smaller female because she showed more spunk! Though both puppies were friendly and playful, the little female was definitely in charge...
