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My vote's for IDW.
When you get down to it, Mirage didn't really have much of dynamic between Shredder and Splinter. Apart from the first time they met (when Shredder murdered Yoshi) I don't recall Spliter interacting with him again. Although I might be mistaken.
The dynamic in IDW was great, they really had a connected history together and they were real enemies.
Souls Winter would be my runner up, mostly because of the deep and thought provoking story and the characterization Shredder had in it (not to mention gorgeous art).
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