I have two Trek 4300's. One is an 03 and the other an 04. I will soon have 10,000 miles on them so i can tell you they are good bikes. Bad shifting is not a symptom of any particular bike. It is a symptom of a bike that needs to have it's derailleur adjusted, cables replaced etc. It is not the bike's fault, so to speak.
A trek 6700 will get you a better, lighter frame and better components. It will also cost you more. As far as discs, that is up to you. I don't like them, as they cost a fair amount and it takes money away from components.