For important games (CDR elimination games, UCL games of importance, La Liga against top teams like Atl?tico, Real, Malaga) the lineup has basically been the same. Messi/Pedro/Iniesta up front - Xavi/Cesc/Busquets in the mid - Alba/Puyol/Pique/Alves/Valdes in the back. This was considered the all around best possible lineup that Barca could field.
There has been some rotation, especially against the lower end teams, to try and get Xavi/Puyol/Iniesta some rest. Mascherano has played quite a lot of games even though he isn't considered 100% of the time for the toughest of games, Adriano prior to his injury at the end of 2012 was playing insane (probably at top 3 in the team level). In addition Sanchez/Song/Villa are in the mid teens for starts and mid twenties for appearances.
In general there has been quite a decent amount of rotation especially against lower end teams. Usually 2-3 people out of the above top 11 would be swapped and rest. I wouldn't blame the play from the last week or two on fatigue. Last season I chalked up the Spring collapse 100% to injuries and fatigue because the team was falling apart. This season has been virtually injury free (knock on wood) apart from Tito being out.
I just think the current top 11 has been ineffective against top teams and is figured out. They play a pretty predictable style, that if it doesn't click 100% it is easy to figure out. Messi tends to be the only person in the box against these teams. Pedro tends to be the all around work horse dragging players out of positions. Cesc tends to push Iniesta into the mid which breaks his left wing position that he has been playing this season and adds more people to the middle cluttering it like crazy especially against teams that play to fill the middle. Also this breaks down the wing play. This team currently needs a real striker like Villa (completely baffled why he hasn't played against top teams) to add penetration into the box. He is also a outside the box shot threat that no one else on the team is. MVP was such a ridiculous front line from 2010/2011 that it should be tried this season. It would send Cesc to the bench and regardless of how good he has been personally, I think the negative effect that it has on Iniesta and general midfield clutter, the drop to bench is needed at least to try it out.
On the defensive end, as good as Alba has been and Alves has been getting better, I am still not settled on the double wingback play. This season has been by far the poorest in defense. Puyol is old and slow, as shown by Di Maria/C.Ronaldo, Pique has never been quick and usually his strength was positioning/technique. Adriano when he plays is exactly like Alba/Alves. Mascherano when he takes over for Puyol has been okay but he is still not a quick defender. Against pace filled teams we literally have nothing. In previous seasons, even though Abidal has been 30+ for a while, he was usually easily our best defender. He is quick, his positioning is rock solid, and he wasn't as offensive minded as Alba that he let his left side open. I really hope Abidal gets to start/sub in soon. He was given the green light to play last week but he hasn't been included on the bench yet.
TL;DR - Overall rotation is there, toughest games usually have the same exact 11.
If you've only seen 2 Barca games then I'm guessing you haven't seen more than 2 RM games this year. Regardless of whether they have the ball a lot or not they excel at counter attacking aggressively at speed, they actually struggle more this year against the weaker teams who don't become stretched if you look at their league results.
The funny part about RM this season has been that they struggled when they dominated the game in possession and were given the ball. In those situations they have been absolutely clueless as to what to do and were unable to create chances. They would usually hover around the middle of the pitch for the entire game and just look flat. On the other hand when RM wasn't the dominant possessor of the ball, they have been absolutely ruthless, it seems it would require them to be less creative and think less about what to do, they would just grab the ball on the break and batter the opposing net.
I am with you on RM progressing against Man Utd. I think they are clicking at the right time of the season and the fact that they were so dominant against Barca in addition to the league being lost, they will field a fairly relaxed 11 for the 2nd La Liga clasico this Saturday. This will allow maximum rest against Man Utd.