Come now, that's a fairly disingenuous explanation on your part. Having Mascherano at CB didn't prevent Barça from winning the CL and 2 league titles in the last three seasons. Of course their defensive issues are coming back to haunt them, but that's because the attacking players aren't capable of covering for them any longer like they have for the past two seasons.
The intriguing thing is that the team has only in the 2nd half of the season started to feel the effects of the tactical shift under Martino. In the 1st half of the season they were very good, but in the last couple of months it's all started to catch up with them. Messi himself has been inconsistent since returning from injury, but the one constant has been the decline in his shot conversion% (basically his clinicalness when finishing) which might have been what papered over the cracks last season. Tata Martino's recent comments after the Atlético 2nd leg, (I'm paraphrasing here), about him not wanting(needing?) Messi in the build-up, are at the heart of the issue IMO. Messi has ALWAYS been a creator first and a finisher second in my eyes. The former is innate in him, the latter hinges far more on his team and his confidence (even in his best seasons). In recent games Messi has cut an isolated figure up front, against Granada he was acting like a traditional nine, trying to get on the end of crosses. It's possible (and maybe even likely) that Martino said what he said because he wanted to protect his player from criticism, but since the last Clásico, Messi has noticeably been struggling to get involved in games (in the losses to Valencia and La Real he was a lot more involved in play). Partially of his own making, his dribbling and passing have been inconsistent for example and off the ball he's almost a non-entity at times, waiting for service and that's just not his game.
I can only speculate, but it seems to me a mix of him being low on confidence, mentally not at 100% (in the sense of him not wanting to risk his fitness for the WC perhaps?), wider issues like Martino's tactics, the general process of decline (which has been going on since 2011, imo), DF/MF base instability having a negative effect on the FWs, poor squad depth and poor squad management, etc.