That's my point, he should have been smart enough to figure that something bigger was happening.
Why, because he might have been smart enough to deduce this in the comics? Nolan very rarely touched upon the detective aspect of Batman in his trilogy of films. While he was smart, there was very little given to us in Batman Begins and The Dark Knight to indicate Batman could have deduced Bane's true intentions. Everything Bane had done in public up to the point where Batman fights him in the sewers had been a direct assault on Bruce Wayne, not Gotham City. So what if he was a former member of the League of Shadows? Bane had been excommunicated and the League of Shadows had been (presumably) annihilated in Batman Begins.