I'd have to say I like the balance of TF2. All the classes have a counter, at least from my own point of view, and it doesn't seem like there are any "super" classes, nor any overpowered combinations of classes. All that's required is a willingness to change your class to fit the situation.
For example, even a poor sniper will do better taking out a heavy on open ground than the most amazing pyro. The pyro should get mowed down before he gets close enough to do any serious damage. The heavy and the sniper aren't overpowered, nor is the pyro underpowered. It's simply a matter of understanding which class is right.
(Qualifier: I also liked the balance in all the versions of NS, and have never really noticed any problems. The majority vote says I lose at balance judgements.)