Messi's "failures" are more down to teams being able to mark him into oblivion because they're not afraid of anyone else on the team. It started with Chelsea in 11/12 and has continued on. If Neymar continues to improve and really become a star then he'll attract more defenders. Right now there are a few different problems at Barcelona.
1. Age - Puyol hasn't played at a high level(barely even at all) since the last time we won the Champions League in 2010/11 and now he's leaving. There have been matches where Mascherano has played brilliantly and so far ahead of the level anyone expects but the sad truth is that he's simply not a true CB and every year I'm absolutely SHOCKED that we STILL don't sign a new CB. Meanwhile, Xavi remains a quality player and absolute Barcelona legend but he lacks two things that he used to have consistently in his prime. Willingness to try world class defense splitting passes and ability to hold his own in defense. Xavi is probably the biggest crutch to Tata's attempt at making Barcelona a multifaceted team in attack. I can't count the amount of times when he's had 2 or 3 of Messi, Pedro, Neymar, etc. making runs into space after gaining possession with a clear chance for a great counter and he slows plays down and passes sideways. He's seemingly obsessed with possession since Pep left and is completely delusional in his claims that we're always better because of meaningless possession(he said we were better against Bayern
)
2. No strength/height/energy - In the last two times Barcelona have been eliminated in the Champions League; they've looked like old men passing the ball around who win only like 15% of all headers, get outrun by EVERYONE, and get pushed off the ball remarkably easily. This was never the case in the Pep era. Why? Well for one, everyone pressed maniacally and the team won the ball back within seconds. Everyone wants to blame Messi for walking(which is part of the problem in some matches but he presses when it's important like vs Man City) but also our midfield doesn't seem to press or care to press very much anymore. Even when Xavi was younger and didn't get embarrassed in defense by anyone with talent; Pep still used to play Seydou Keita in away matches in the Champions League to provide some extra steel in midfield. Now the team doesn't have anyone in that mold of Keita/Yaya and Song has been a failed experiment or perhaps not properly utilized. Cruyff just said it that we have no physical players anymore and that hurts the team greatly. This sport relies a lot of technical ability but it's still important to be in great physical shape and I feel our team lacks that.
3. Motivation - Atletico 100% deserved to win and in fact deserved to win by more than one goal at the Vicente Calderon. They wanted it WAY more than Barcelona. They won every loose ball, won almost every header, etc. My theory is that too many players at Barcelona have won everything there is to win so that while they may still have desire to win; some of that internal fire has been dimmed. Hopefully some new signings of players who have never won the Champions League will reinvigorate the squad.