One suggestion about the stats system: How about the more you do something the better you get at it. I mean, you'd have to have training to gain the skill, but then, as you use it and maybe have the option to practice it when you're in hyperspace, it starts going up. So like picklocking would be faster for you, hacking would be faster and not noticed as much, shots would be more accurate and faster, etc.
Vader's wife was very pregnant when she died 19 years ago. All of a sudden a 19 year old who is very strong in the force and has a distinct resembalance to him in his younger days rolls in from Vader's home planet with his old Master Obi-Wan (Who was the ONLY other person preset at the time his wife died. And to boot, the kid's last name is Skywalker.
So in answer to your question, he knew Luke was his son because his name is Darth Vader, and not Darth Retard.
-Forum post on why Vader knew Luke was his son.