Federer has never been a great 2nd serve returner, his 1st serve returns are still among the best in the business. Maybe just behind Djokovic.
He did hit 5 return winners and some other couple of returns that Berdych couldn't control but I agree his 2nd serve returns were poor, very passive.
For example out of the 4 match points, 2 of them were on 2nd serves. The first time Fed hit a flat BH that landed in Berdych service box. The 2nd one Fed hit the chip return that won him the match in the end but it was a chicken shot. Insted of being agressive and taking faith in his own hands he was just asking Berdych the questions: "can you hit a winner while being so close to the net at mp down?"