Damn. They both have so much in the area of awesome that there's no clear winner objectively. The OT Shredder has the voice of Uncle Phil, a sense of humor, is a technological genius, and a superb combatant. He's sorta ineffective when it comes to defeating the turtles...

... BUT he does understand how to annoy and hinder them! That's worth some points.
The live-action Shredder is a badass through-and-through. He takes himself and life in general very seriously, is about as masculine as a man can get, and beats the hell out of the four turtles with a notably fluid ease. This Shredder answers to NOBODY! There's no way this version would even take orders from a pink brain warlord from another dimension. That razor-studded ensemble attests to his fine taste in fashion, and it is as menacing as his gruff voice.
My vote goes to the live-action Shredder, though they are both great.