I think the formation Barcelona started with (which looks like a diamond) makes them too dependent on Messi in the playmaker position. Sure he's a brilliant player but he wasn't at his best Wednesday. Fortunately their fullbacks provide width like nobody else, so it gives them an alternate attack in the formation. I think that with the rise and rise of Messi, the team is becoming more dependent on him.
Arsenal did a lot right this game, but their offside line, while the right idea, wasn't executed particularly well. They were lucky quite a few times. Like the 2 goals Ibra scored at the Emirates last year, they played the high line, but then gave the Barca midfielder with the ball too little pressure, allowing him to pick out the through ball.
Offensively Arsenal wasted too much time trying to short pass their way through midfield, which just invited pressure and kept costing them possession. When they played longer balls to the front lines. I think that's why Bendtner was put on. They bypassed the pressure and exposed Barca’s weak(ish) defence. The Arsenal Plan B highlighted in the recent Everton game paid dividends here, under slightly different circumstances. This was augmented by Wilshere’s runs through midfield. I don't know why I never realised how strong he is when running with the ball.
Finally I think Barca, as good as they are, are becoming a little too predictable for top level competitors. Pep will have to figure out a way to adjust his formation or tactics for Camp Nou. Arsenal is still obviously a work in progress, but their progress is undeniable.