Iniesta has certainly been better than Messi and goals scored doesn't change a thing.
Teams concede goals, and teams score them. When Messi has the last touch to put the ball in the net, even after outstanding athletic plays, it has been a TEAM EFFORT.
You're reducing Messi to a mere goal-scorer in the way you describe him. I would actually agree with that for 2013 but not for the entire season. You reduce goal-scoring to a team effort and something that doesn't require too much skill (which is ridiculous considering how difficult it is for our other forwards to score). On the other hand, you make it sound like Iniesta alone has created a feeling of hopelessness in the other team (and you don't even have any evidence for that because that is unquantifiable and can never be proved/measured). Guess what, possession is far more team-based than scoring goals. You really need to look back at our earlier fixtures to see how important Messi was then.
How many times has Messi scored after Iniesta had spent the match doing a much better job of helping the opposition along toward mental/physical exhaustion and a feeling of hopelessness?
Not many. Opposition are certainly not tiring out towards the end of the game as they used to. In addition to that, Messi has not been scoring many late goals this season. And when he has (like vs Granada or vs Osasuna), Iniesta has either been on the bench or had a poor game. Interestingly, those were games where many people would agree that Messi literally saved the team by earning 3 points.
I'm re-iterating - but the best evidence you can find to suggest Messi's superiority is the man of the match thread because the opinions are recorded right after the game. When we have these hypothetical arguments now, recent performances will always cloud our judgment. I'm not gonna lie - I also felt that Iniesta has been better than Messi this season when I read this thread yesterday. But then I actually thought about it.
And obviously, statistically Iniesta is no match for Messi. So both subjectively and objectively, the evidence points to Messi.
You can obviously always question the methods (lot of people on this forum like their own opinions more than whoscored), a lot of people will also disregard the man of the match thread for being filled with Messi "fanboys". In that case, I don't actually have any other evidence to either prove or disprove that Messi has been better than Iniesta.