To be honest, I can understand why Bayern are super-fit. They have a 34 game league, one cup competition and have quality second choice players who have the quality to win them games while many of the first choices are being rested.
But, the Barcelona teams' fitness levels are insane. They press hard, keep moving to receive passes and often outrun their opponents and the same fucking core of players have been doing it playing every game in last five years. Look at Messi, for instance, he just never misses a minute of games!
However, as a counter-point, I think, it would be very very difficult to cover-up something clearly wrong that involves this many people. There are dozens of players going in and out of the clubs mentioned, may of them in acrimonious circumstances, and some information would have gotten out somehow if systematic doping has been going on. It is however possible that specific "trusted" players are being "helped" or the players are not fully aware of what is being fed/injected to them.
According to an article here -
A poll in FourFourTwo recently, which was undertaken by 100 anonymous footballers in Britain, revealed that 13% of those individuals asked knew of players who had taken performance enhancing drugs. Arsene Wenger also spoke this season about his suspicions of doping in football, saying that he believed it was much more widespread than was being reported and that he couldn’t believe FIFA test hundreds of players at World Cups yet find “zero problems”.