They've missed Abidal the most. Whether against Chelsea or Real Madrid, having Abidal at LB would've definitely prevented Drogba from scoring at Stamford and Ronaldo at the Camp Nou.
Guardiola's insistence on playing the one-trick-pony Tello was another big mistake. He's played 2 games and he's already been found out, a step over and run towards the by-line to cross. And when's he presented with a one-on-one, he always plays it to the far side. An off-form Pedro would've still been a much other option as he has already scored in a Champions League final before so he's used to the pressure and expectations.
Mascherano for all his defending skills, is terrible at CB. His positioning is awful and is responsible for Drogba and Ronaldo's goals. Also another goal against Milan when he ruined the offside trap.
Last point, fatigue played a huge role in Barca's week, it seemed obvious that around the 70-minute mark, all of Barca's players had run out of steam. That's what you get when you insist on playing Messi for 90 minutes when you're 2-3 goals up against weak opposition in the league.