We can all speculate about the turmoil Barca were under, and how that could have affected the team etc. We can also speculate as to the mental and physical state of Atletico before the match. But those would only be that, speculations.
What we can appreciate is the very much apparent change in the way the team approached and played that game, which was percolating even from the previous game vs Elche in Copa. Fullbacks at the halfway line, many times playing inside as DMs. Midfielders interchanging with the wingers. Messi dragging the fullback and Rakitic attacking the space left behind to break the back 4. The way Barca played definitely created some trouble for Atletico and caught them very much unprepared.
Simeone playing Gamez at left back being a right footed player was very much a planned attempt to stop Messi, whom he knew was going to play in the wing, from cutting inside to his left foot. The dynamic of Messi, Rakitic and the fullbacks totally undid what Simeone had planned. From that wing the game was broken and it had very much to do with the way the team was set up to play. All 3 goals were borne from this tactic.
Look here. This is the moments that preceded the first goal vs Atletico. Look at the shape. Alves and Alba almost in line with Busquets, Alves tucked inside not hugging the wing, almost like another midfielder. Both Rakitic and Iniesta preoccupying the defense. Now also look at Messi in relation to Neymar. Neymar is almost level with Suarez, but Messi is deeper.
Immediately after, Alves passed to Messi. Notice again, Neymar is almost level with Suarez but Messi is deeper. Notice also how Messi receiving the ball deeper drags Gamez away from the back 4 formation, also drags Koke to try to double team Messi. Notice thirdly how Rakitic immediately attacks the space left by Gamez, dragging both Thiago and Godin away from their formations.
This is the result. Four defenders for 2 players in the right wing. The back 4 defensively is broken.
Rakitic does well to release the ball back to Alves and watch how unorganized Atletico is left by the simple move of Messi receiving deeper, dragging Gamez, and Rakitic attacking the space. Godin is out of position and sprinting to recover. Gamez left guarding no one. Thiago and Koke are scrambling. A nice penetrating pass from Alves to Messi creates all sorts of havoc and leads to the goal in which both Suarez and Neymar are 1v1 in the box vs Gimenez and Juanfran.
The other 2 goals were from similar dynamics.
I've no doubt Simeone will adjust to this and then we'll see. I also still have doubts whether he'll field a starting 11 or again another B side like he did in the first leg vs Real Madrid. In any case, there is only so much he can do to counter Messi's presence. Maybe he'll pull Thiago from the middle to double team him with Koke, instead of pulling the fullback, but that leaves the midfield expose. Maybe he's willing to sacrifice that. Give the ball to the lesser midfield and have them beat you vs allowing Messi to beat you instead.