Mourinho is not the kind of coach that has tons of different formations to choose from. In his first season with Real Madrid, we saw the three-man midfield more than once, with Khedira, Lass and Xabi Alonso. But last season, the Portuguese coach decided to leave that option out.
He didn't have as many midfielders, though. With Essien and Khedira, the 4-3-3 formation against top European teams like Manchester City could be a very good choice, even more if we consider it's still September. Mancini's team is used to having most of the possession against the English teams in the Premier League, but the "citizens" often struggle with it. If Khedira and Essien or Modric start alongside Xabi Alonso, Real Madrid would be able to steal the ball more quickly, but Mourinho's team would not have an easy time when Manchester City's defense sets down.
Given that Manchester City is a very dangerous team in the counterattack with Tévez, Agüero, Balotelli, Silva or Nasri as the best examples of that, it could be better for Real Madrid to change Mancini's plan. Give them the ball, don't let them counterattack and defend every possession with the three-man midfield. Real Madrid will have its chance to convert off one counter sooner rather than later.