2012 Shredder >>>> 2003 Shredder
Mainly because he inflicted more relatively long-lasting consequences.
>Mutating/Brainwashing Karai
>Giving April to the Kraang
>Killing Splinter
>Beating Leonardo to near-death and driving the Turtles on the run
>The whole black hole incident
But also because he had a more personal connection to Splinter/the turtles.
AND also because he was way more relatively threatening in a fight than 2003. Remember the 1v8?