And yes it's odd that Berdych has more confidence vs Federer these days than vs Nadal. Berdych's game is almost perfect to beat Nadal. He likes hitting up high and is one of the best guys on the tour at punishing high bouncing balls or weak second serves with both his forehand and backhand.
I can remember their early matches, he really was comfortable against Nadal.
And what has mostly changed in Nadal's game since then is ... the depth of his shots.
I've already said that but I disagree with the "one definition" of "big hitters" for Berdych on one side, Del Potro and Söderling on the other side.
They are very different : Berdych doesn't have Del Po or Söderling's power to hit several deep and powerful shots in a row from the back of the court.
For them power is just natural. Berdych likes to accelerate, on rather short balls, which is very different.
And as I said, Nadal's main improvement comparing to his young time has been imo the depth of his shots, which imo explains that he gives more problems to Berdych.
Moreover, Nadal's serve has improved and actually Berdych really has problems to be effective on return on Nadal's serve.