Hi!
This being one of my first posts please excuse any mistakes such as any picture sizes.
Note that all 2012 pictures have been pulled from Brickipedia as I have not been able to get any new Batman sets.
The Batman (2006)
from 7781, 7783, 7785
The Batman (2012)
from 6863, 6864
As you can see above..
he 2006 version has a larger Bat-symbol on his chest and thicker chest muscles printing. While the new Superheroes version has some chest muscle showing above the Bat-symbol and has his utility belt in the early pouch version while the 2006 Batman has his utility belt in the capsule version. With Lego, adding more detail than previously to the minifigures, the newer one has back printing and a double sided head.
I can't seem to add anymore photos to this post as my upload quota has been maxed out? Not really sure how that works though, as I have more comparisons to add.
-Fatfrog