Is Messi all Real Madrid should worry about? Of course not, but if Mourinho's defense stops the Argentinian star, his team will have a much easier path to the Copa del Rey Final. Neither Alexis Sánchez nor David Villa are helping Messi or their team much, but Iniesta and Pedro are in great shape and Barça's franchise player is certainly making profit out of that.
Even though technically Vilanova's team is having what almost is a perfect season, there still are some questions about the fragility of the defensive system. Piqué isn't (and never will be) the center back that surprised everyone back in 2009. He single-handedly stopped Cristiano Ronaldo in Pellegrini's only season with Real Madrid, but he now needs the help of Puyol or Mascherano, and neither one of them can keep up with Cristiano Ronaldo's pace.
Alves isn't as good as he was a couple of years ago neither. It seems that he can only focus on one aspect of the game now. Adriano is the player that is having good minutes. His ability to play in both of Barcelona's wings is very useful for Vilanova, and the Brazilian defender has scored some beautiful and important goals this season.
It seems that, while Guardiola's Barcelona was all about Xavi and Messi, Tito's own team currently relies more on Busquets and the reigning Ballon D'Or winner. Busquets is both distributing the ball well but also executing Barcelona's pressure brilliantly by being the team's last defender before the opposition faces the defensive line. It seems necessary to find Busquets' back in order to enjoy good counterattacking chances.
One way or another, Barcelona is indeed having a perfect season. While they don't seem as imposing as they were under Guardiola, they still have Messi. That's a massive wildcard. But, it appears that with Messi and Ronaldo out of the game, Real Madrid would have the edge over this Vilanova's Barcelona.