That was then, when Guardiola ruled roost, but clubs have caught up with them and when you analyze what the result in the Copa del Rey means, a 1-3 loss to a Mourinho-led side that is 16 points back of a long-lost league title, and let's also not forget to mention what AC Milan was allowed to accomplish in the Champions League, then there are definite concerns for FC Barcelona.
Administration: Sandro Rosell has entrusted himself with the legacy of FC Barcelona and he has the genetic makeup of a long-term supporter going back decades, but he is not and never will be Joan Laporta. For all his faults Laporta would have found a way to maintain his administrative board and used his considerable acumen in front of the media to take pressure off his side. Rosell may have a better set of Barca DNA coursing through his veins but he struggles to place his stamp on the club in comparison.
Coaching: hiring Tito Vilanova was a stroke of genius. Pep Guardiola's oldest friend at the club was known previously as the recipient of a Jose Mourinho eye gouge but what we all neglected to see was how important he was to their otherworldly success. When he succumbed for the second time to cancer earlier in the year it was obvious that the forgotten element in their success has been their coaching. They can't just throw out the ball and let the players play. Jordi Roura may be the sort of leader that can continue the legacy of Cruyff at the club, and Tito spoke highly of him when he chose him for his second at the beginning of the campaign, but it's clear that his words don't carry the same weight with the players that Tito's do; he's an interim or caretaker or whatever you want to label it as. What it means is that the unfortunate Roura is in the unenviable position of guiding the FC Barcelona ship on someone else's watch.
Goalkeeping: it is no coincidence that this odd run of form for Barcelona lies also at the feet of Victor Valdez. At the restart the Barca keeper stated that he would seek other options for next season. Since then their domestic and European form has been spotty. Can we also shine a spotlight on the fact that Real Madrid use their first team keeper for every competition and Barcelona don't? Pinto is a serviceable keeper but FC Barcelona have not identified a consistent backup let alone a replacement for Victor Valdez. Advantage here for Real Madrid.
Defense: there is a ton of criticism being handed down at FC Barcelona for their inability to handle the Real Madrid counterattack. That's not a problem in the grand scheme of things. Barca's defense is reliant on their mid-field's ability to recover balls on their opponent's side of the pitch. If they can't then they need mobility and decisiveness in their center-backs to stop opponent's counters. Gerard Pique is fine in that role but Carles Puyol is 5 years past his best in support. That is red flag number one. Red flag number two is their reliance on Javier Mascherano as a long-term solution who is obviously one of the best defensive midfielders in the world but he is playing out of position; he doesn't have the instincts of a center-back.
Midfield: in their midfield under Guardiola, when they were at their best, Busquets was the enforcer and both Xavi and Iniesta ran rampant in the center of midfield supplying balls to their attack. When you add Cesc Fabregas, who was once projected as Xavi Hernandez's future replacement but because of his training at Arsenal FC became much more of a support striker rather than a deep-lying play-maker, you separate your most important cogs away from each other. As good as Cesc is, he interrupts the pipeline between Xavi and Inesta and slows the circulation of balls in midfield. It's not a problem per-se, there are many ways to skin a cat in football and Barcelona excel at maintaining possession against less talented sides, but when faced with clubs that plug the center-midfield and force Barca wide (like Sevilla last weekend or Real Madrid midweek) then Cesc becomes irrelevant when playing with Iniesta and Xavi. It's no wonder that the only goal was scored by wide-man Jordi Alba just like the weekend's win was engendered by their wide-play in the second half.
Attack: many will condemn the play of Lionel Messi in this loss to Real Madrid. He was found out in this role that both interfered with Cesc in midfield and also interfered with David Villa in attack. Fact is that they need to decide what is going to be their plan A, B, C or whatever. Lionel Messi cannot coexist with David Villa. He can play with and through Cesc but El Guaje needs the more traditional service that they have not relied on since Samuel Eto'o left for Italy (let alone Russia). What they need is width no matter who plays in the center. When Barca were great they had disciplined play on the wing both in attack and defense, full-backs and wingers overlapping and helping out on counterattacks, but Jordi Alba and Dani Alves are not great at tracking back. Pedro is not as effective if he is isolated on the right, Tello is too green to be a consistent threat on the left, and the one player that they bought to take pressure off Lionel Messi on the wings and allow him space along the front-line is Alexis Sanchez who has never adapted himself to the possession game that FC Barcelona plays; he's a Marcelo Bielsa winger who plays quickly in space and not someone who fits the Barcelona system very well.
It´s still an enviable position to be in. This is still one of a handful of sides to make that illustrious all-time group of mythical clubs that defined their era. No one would be talking about them in hushed tones and wistful sighs if they weren´t, but Real Madrid have clearly caught up with them and so have many others.