I too think Nadal takes the match, though Federer is in the lead with the winning of two sets. When the odds got closer for both the players predicted that Nadal wins and have used 0.1btc in the wallet for gambling.
Federer again used the medical timeout to get back to good shape and change the momentum. It is a good trick to use, especially when the opponent is fired up. Once you slow the game down by taking timeout its hard for the opponent to keep up that high intensity he had before. Federer might genuinely have had an injury and thats why he took a time out but I think it was more tactical than medical. He did the same thing during his last match and came back stronger against the opponent.